diff --git a/packages/plugins/@nocobase/plugin-client/src/server/__tests__/desktopRoutes.test.ts b/packages/plugins/@nocobase/plugin-client/src/server/__tests__/desktopRoutes.test.ts
index 330b1141ba0..458bc394254 100644
--- a/packages/plugins/@nocobase/plugin-client/src/server/__tests__/desktopRoutes.test.ts
+++ b/packages/plugins/@nocobase/plugin-client/src/server/__tests__/desktopRoutes.test.ts
@@ -9,6 +9,7 @@
 
 import Database, { Model, Repository } from '@nocobase/database';
 import { createMockServer, MockServer } from '@nocobase/test';
+import CleanOrphanFlowRouteModelsMigration from '../migrations/202605121200-clean-orphan-flow-route-models';
 
 describe('desktopRoutes:listAccessible', () => {
   let app: MockServer;
@@ -290,3 +291,188 @@ describe('desktopRoutes', async () => {
     expect(rolesDesktopRoutes.length).toBe(0);
   });
 });
+
+describe('desktopRoutes flow model cleanup', () => {
+  let app: MockServer, db: Database, desktopRoutesRepo: Repository;
+  let flowRepo: any, usageRepo: any;
+
+  const buildReferenceOptions = (templateUid: string) => ({
+    use: 'ReferenceBlockModel',
+    stepParams: {
+      referenceSettings: {
+        useTemplate: {
+          templateUid,
+          templateName: `name-${templateUid}`,
+          mode: 'reference',
+        },
+      },
+    },
+  });
+
+  const createTemplate = async (uid: string) => {
+    await app
+      .agent()
+      .resource('flowModelTemplates')
+      .create({
+        values: {
+          uid,
+          name: uid,
+          targetUid: 'target-block',
+        },
+      });
+  };
+
+  const saveRouteTreeWithReferenceBlock = async (routeUid: string, referenceUid: string, templateUid: string) => {
+    await app
+      .agent()
+      .resource('flowModels')
+      .save({
+        values: {
+          uid: routeUid,
+          use: 'RouteModel',
+          subModels: {
+            page: {
+              uid: `${routeUid}-page`,
+              use: 'RootPageModel',
+              subModels: {
+                grid: {
+                  uid: referenceUid,
+                  ...buildReferenceOptions(templateUid),
+                },
+              },
+            },
+          },
+        },
+      });
+  };
+
+  const createSchemaRouteRoot = async (routeUid: string) => {
+    await flowRepo.create({
+      values: {
+        uid: routeUid,
+        name: routeUid,
+        schema: {
+          use: 'RouteModel',
+        },
+      },
+    });
+  };
+
+  const countUsage = (filter: Record<string, any>) => {
+    return usageRepo.count({ filter });
+  };
+
+  beforeEach(async () => {
+    app = await createMockServer({
+      registerActions: true,
+      plugins: [
+        'error-handler',
+        'client',
+        'field-sort',
+        'acl',
+        'ui-schema-storage',
+        'system-settings',
+        'data-source-main',
+        'data-source-manager',
+        'flow-engine',
+        'ui-templates',
+      ],
+    });
+    db = app.db;
+    desktopRoutesRepo = db.getRepository('desktopRoutes');
+    flowRepo = db.getRepository('flowModels');
+    usageRepo = db.getRepository('flowModelTemplateUsages');
+
+    await flowRepo.create({
+      values: {
+        uid: 'target-block',
+        options: {
+          use: 'TargetBlock',
+        },
+      },
+    });
+  });
+
+  afterEach(async () => {
+    await app.destroy();
+  });
+
+  it('should remove child route flow model tree and template usages when deleting a parent desktop route', async () => {
+    await createTemplate('tpl-route-cleanup');
+    const group = await desktopRoutesRepo.create({
+      values: {
+        title: 'group',
+        type: 'group',
+      },
+    });
+    await desktopRoutesRepo.create({
+      values: {
+        title: 'child page',
+        type: 'flowPage',
+        parentId: group.get('id'),
+        schemaUid: 'route-cleanup',
+      },
+    });
+    await saveRouteTreeWithReferenceBlock('route-cleanup', 'ref-route-cleanup', 'tpl-route-cleanup');
+
+    expect(await countUsage({ templateUid: 'tpl-route-cleanup', modelUid: 'ref-route-cleanup' })).toBe(1);
+
+    await desktopRoutesRepo.destroy({
+      filterByTk: group.get('id'),
+    });
+
+    expect(await flowRepo.findOne({ filter: { uid: 'route-cleanup' } })).toBeFalsy();
+    expect(await flowRepo.findOne({ filter: { uid: 'route-cleanup-page' } })).toBeFalsy();
+    expect(await flowRepo.findOne({ filter: { uid: 'ref-route-cleanup' } })).toBeFalsy();
+    expect(await countUsage({ templateUid: 'tpl-route-cleanup', modelUid: 'ref-route-cleanup' })).toBe(0);
+
+    const destroyTemplateResp = await app.agent().resource('flowModelTemplates').destroy({
+      filterByTk: 'tpl-route-cleanup',
+    });
+    expect(destroyTemplateResp.status).toBe(200);
+  });
+
+  it('should clean orphan RouteModel trees and stale usages in migration', async () => {
+    await createTemplate('tpl-orphan-route');
+    await desktopRoutesRepo.create({
+      values: {
+        title: 'active page',
+        type: 'flowPage',
+        schemaUid: 'active-route',
+      },
+    });
+    await desktopRoutesRepo.create({
+      values: {
+        title: 'active schema page',
+        type: 'flowPage',
+        schemaUid: 'active-schema-route',
+      },
+    });
+
+    await saveRouteTreeWithReferenceBlock('active-route', 'ref-active-route', 'tpl-orphan-route');
+    await saveRouteTreeWithReferenceBlock('orphan-route', 'ref-orphan-route', 'tpl-orphan-route');
+    await createSchemaRouteRoot('orphan-schema-route');
+    await usageRepo.create({
+      values: {
+        uid: 'usage-missing-route-model',
+        templateUid: 'tpl-orphan-route',
+        modelUid: 'missing-route-model',
+      },
+    });
+
+    expect(await countUsage({ templateUid: 'tpl-orphan-route' })).toBe(3);
+
+    const migration = new CleanOrphanFlowRouteModelsMigration({ db, app } as any);
+    await migration.up();
+
+    expect(await flowRepo.findOne({ filter: { uid: 'active-route' } })).toBeTruthy();
+    expect(await flowRepo.findOne({ filter: { uid: 'active-schema-route' } })).toBeTruthy();
+    expect(await flowRepo.findOne({ filter: { uid: 'ref-active-route' } })).toBeTruthy();
+    expect(await flowRepo.findOne({ filter: { uid: 'orphan-route' } })).toBeFalsy();
+    expect(await flowRepo.findOne({ filter: { uid: 'orphan-schema-route' } })).toBeFalsy();
+    expect(await flowRepo.findOne({ filter: { uid: 'ref-orphan-route' } })).toBeFalsy();
+    expect(await countUsage({ templateUid: 'tpl-orphan-route', modelUid: 'ref-orphan-route' })).toBe(0);
+    expect(await countUsage({ templateUid: 'tpl-orphan-route', modelUid: 'missing-route-model' })).toBe(0);
+    expect(await countUsage({ templateUid: 'tpl-orphan-route', modelUid: 'ref-active-route' })).toBe(1);
+  });
+});
diff --git a/packages/plugins/@nocobase/plugin-client/src/server/migrations/202605121200-clean-orphan-flow-route-models.ts b/packages/plugins/@nocobase/plugin-client/src/server/migrations/202605121200-clean-orphan-flow-route-models.ts
new file mode 100644
index 00000000000..7f6dad65ae7
--- /dev/null
+++ b/packages/plugins/@nocobase/plugin-client/src/server/migrations/202605121200-clean-orphan-flow-route-models.ts
@@ -0,0 +1,117 @@
+/**
+ * This file is part of the NocoBase (R) project.
+ * Copyright (c) 2020-2024 NocoBase Co., Ltd.
+ * Authors: NocoBase Team.
+ *
+ * This project is dual-licensed under AGPL-3.0 and NocoBase Commercial License.
+ * For more information, please refer to: https://www.nocobase.com/agreement.
+ */
+
+import { Migration } from '@nocobase/server';
+import * as _ from 'lodash';
+
+const parseOptions = (value: any) => {
+  if (!value) return {};
+  if (typeof value === 'string') {
+    try {
+      return JSON.parse(value);
+    } catch (error) {
+      return {};
+    }
+  }
+  return value;
+};
+
+const isRouteModelOptions = (value: any) => {
+  const options = parseOptions(value);
+  return options?.use === 'RouteModel' || options?.schema?.use === 'RouteModel';
+};
+
+export default class extends Migration {
+  on = 'afterLoad';
+
+  async up() {
+    if (
+      !this.db.hasCollection('desktopRoutes') ||
+      !this.db.hasCollection('flowModels') ||
+      !this.db.hasCollection('flowModelTreePath')
+    ) {
+      return;
+    }
+
+    await this.db.sequelize.transaction(async (transaction) => {
+      const desktopRoutesRepo = this.db.getRepository('desktopRoutes');
+      const flowRepo = this.db.getRepository('flowModels') as any;
+      const treePathRepo = this.db.getRepository('flowModelTreePath');
+
+      const desktopRoutes = await desktopRoutesRepo.find({ fields: ['schemaUid'], transaction });
+      const routeSchemaUids = new Set(desktopRoutes.map((route) => route.get('schemaUid')).filter(Boolean));
+
+      const flowModels = await flowRepo.find({ fields: ['uid', 'options'], transaction });
+      const routeModelUids = flowModels
+        .filter((model) => isRouteModelOptions(model.get('options')))
+        .map((model) => model.get('uid'))
+        .filter(Boolean);
+
+      if (routeModelUids.length) {
+        const childRouteModels = new Set<string>();
+        for (const chunk of _.chunk(routeModelUids, 500)) {
+          const parentPaths = await treePathRepo.find({
+            filter: {
+              descendant: {
+                $in: chunk,
+              },
+              depth: 1,
+            },
+            fields: ['descendant'],
+            transaction,
+          });
+          for (const path of parentPaths) {
+            const descendant = path.get('descendant');
+            if (descendant) {
+              childRouteModels.add(descendant);
+            }
+          }
+        }
+        const orphanRouteModelUids = routeModelUids.filter(
+          (uid) => !routeSchemaUids.has(uid) && !childRouteModels.has(uid),
+        );
+
+        for (const uid of orphanRouteModelUids) {
+          await flowRepo.remove(uid, { transaction });
+        }
+      }
+
+      if (this.db.hasCollection('flowModelTemplateUsages')) {
+        const usageRepo = this.db.getRepository('flowModelTemplateUsages');
+        const usages = await usageRepo.find({ fields: ['modelUid'], transaction });
+        const usageModelUids = _.uniq(usages.map((usage) => usage.get('modelUid')).filter(Boolean));
+
+        for (const chunk of _.chunk(usageModelUids, 500)) {
+          const existingModels = await flowRepo.find({
+            fields: ['uid'],
+            filter: {
+              uid: {
+                $in: chunk,
+              },
+            },
+            transaction,
+          });
+          const existingUids = new Set(existingModels.map((model) => model.get('uid')).filter(Boolean));
+          const missingUids = chunk.filter((uid) => !existingUids.has(uid));
+
+          if (missingUids.length) {
+            await usageRepo.destroy({
+              filter: {
+                modelUid: {
+                  $in: missingUids,
+                },
+              },
+              transaction,
+            });
+          }
+        }
+      }
+    });
+  }
+}
diff --git a/packages/plugins/@nocobase/plugin-client/src/server/server.ts b/packages/plugins/@nocobase/plugin-client/src/server/server.ts
index 2d388c7f78b..94d4ed1e667 100644
--- a/packages/plugins/@nocobase/plugin-client/src/server/server.ts
+++ b/packages/plugins/@nocobase/plugin-client/src/server/server.ts
@@ -188,15 +188,53 @@ export class PluginClientServer extends Plugin {
         instance.allowNewMenu === undefined ? ['admin', 'member'].includes(instance.name) : !!instance.allowNewMenu,
       );
     });
-    this.db.on('desktopRoutes.afterDestroy', async (instance: Model, { transaction }) => {
-      const r = this.db.getRepository('flowModels');
-      if (r) {
-        await r.destroy({
+
+    const collectDesktopRouteSchemaUids = async (instance: Model, transaction?: Transaction) => {
+      const routeRepo = this.db.getRepository('desktopRoutes');
+      const schemaUids = new Set<string>();
+      const pendingIds: Array<string | number> = [];
+      const rootId = instance.get('id');
+      const rootSchemaUid = instance.get('schemaUid');
+
+      if (rootSchemaUid) {
+        schemaUids.add(rootSchemaUid);
+      }
+      if (rootId) {
+        pendingIds.push(rootId);
+      }
+
+      while (pendingIds.length) {
+        const routes = await routeRepo.find({
+          fields: ['id', 'schemaUid'],
           filter: {
-            uid: instance.get('schemaUid'),
+            parentId: {
+              $in: pendingIds.splice(0, pendingIds.length),
+            },
           },
           transaction,
         });
+        for (const route of routes) {
+          const schemaUid = route.get('schemaUid');
+          const id = route.get('id');
+          if (schemaUid) {
+            schemaUids.add(schemaUid);
+          }
+          if (id) {
+            pendingIds.push(id);
+          }
+        }
+      }
+
+      return Array.from(schemaUids);
+    };
+
+    this.db.on('desktopRoutes.beforeDestroy', async (instance: Model, { transaction }) => {
+      const r = this.db.getRepository('flowModels') as any;
+      if (r?.remove) {
+        const schemaUids = await collectDesktopRouteSchemaUids(instance, transaction);
+        for (const schemaUid of schemaUids) {
+          await r.remove(schemaUid, { transaction });
+        }
       }
     });
     this.db.on('desktopRoutes.afterCreate', async (instance: Model, { transaction }) => {
diff --git a/packages/plugins/@nocobase/plugin-flow-engine/src/server/repository.ts b/packages/plugins/@nocobase/plugin-flow-engine/src/server/repository.ts
index b8c61eb52a2..8dcb096f327 100644
--- a/packages/plugins/@nocobase/plugin-flow-engine/src/server/repository.ts
+++ b/packages/plugins/@nocobase/plugin-flow-engine/src/server/repository.ts
@@ -456,6 +456,29 @@ export class FlowModelRepository extends Repository {
       return;
     }
 
+    const descendants = (await this.database.sequelize.query(
+      this.sqlAdapter(`SELECT descendant FROM ${this.flowModelTreePathTableName} WHERE ancestor = :uid`),
+      {
+        type: 'SELECT',
+        replacements: {
+          uid,
+        },
+        transaction,
+      },
+    )) as Array<{ descendant?: string }>;
+    const uids = descendants.map((row) => row.descendant).filter(Boolean) as string[];
+
+    if (uids.length) {
+      await this.database.emitAsync(
+        `${this.collection.name}.beforeRemoveTree`,
+        {
+          rootUid: uid,
+          uids,
+        },
+        options,
+      );
+    }
+
     await this.database.sequelize.query(
       this.sqlAdapter(`DELETE FROM ${this.flowModelsTableName} WHERE "uid" IN (
             SELECT descendant FROM ${this.flowModelTreePathTableName} WHERE ancestor = :uid
diff --git a/packages/plugins/@nocobase/plugin-ui-templates/src/server/__tests__/template-usage.test.ts b/packages/plugins/@nocobase/plugin-ui-templates/src/server/__tests__/template-usage.test.ts
index cbbc92e3ca1..117151f1300 100644
--- a/packages/plugins/@nocobase/plugin-ui-templates/src/server/__tests__/template-usage.test.ts
+++ b/packages/plugins/@nocobase/plugin-ui-templates/src/server/__tests__/template-usage.test.ts
@@ -150,6 +150,65 @@ describe('ui templates and usages', () => {
     expect(destroyResp2.status).toBe(200);
   });
 
+  it('should remove target tree usages when template is destroyed', async () => {
+    const agent = app.agent();
+    await agent.resource('flowModelTemplates').create({
+      values: {
+        uid: 'tpl-block',
+        name: 'Block Template',
+        targetUid: 'target-block',
+      },
+    });
+
+    const savePopupTargetResp = await agent.resource('flowModels').save({
+      values: {
+        uid: 'popup-template-root',
+        use: 'PopupActionModel',
+        subModels: {
+          content: [
+            {
+              uid: 'popup-ref-block',
+              ...buildOptions('tpl-block'),
+            },
+          ],
+        },
+      },
+    });
+    expect(savePopupTargetResp.status).toBe(200);
+
+    expect(await countUsage({ templateUid: 'tpl-block', modelUid: 'popup-ref-block' })).toBe(1);
+    const blockTplResp = await agent.resource('flowModelTemplates').get({
+      filterByTk: 'tpl-block',
+    });
+    expect(blockTplResp.status).toBe(200);
+    const blockTpl = blockTplResp.body?.data || blockTplResp.body;
+    expect(blockTpl?.usageCount).toBe(1);
+
+    const popupTplResp = await agent.resource('flowModelTemplates').create({
+      values: {
+        uid: 'tpl-popup',
+        name: 'Popup Template',
+        targetUid: 'popup-template-root',
+        type: 'popup',
+      },
+    });
+    expect(popupTplResp.status).toBe(200);
+
+    const destroyResp = await agent.resource('flowModelTemplates').destroy({
+      filterByTk: 'tpl-popup',
+    });
+    expect(destroyResp.status).toBe(200);
+
+    expect(await countUsage({ templateUid: 'tpl-block', modelUid: 'popup-ref-block' })).toBe(0);
+    expect(await flowRepo.findNodesById('popup-template-root', { includeAsyncNode: true })).toHaveLength(0);
+    const blockTplRespAfterDestroy = await agent.resource('flowModelTemplates').get({
+      filterByTk: 'tpl-block',
+    });
+    expect(blockTplRespAfterDestroy.status).toBe(200);
+    const blockTplAfterDestroy = blockTplRespAfterDestroy.body?.data || blockTplRespAfterDestroy.body;
+    expect(blockTplAfterDestroy?.usageCount).toBe(0);
+  });
+
   it('should sync template name/description to reference blocks on template update', async () => {
     const agent = app.agent();
     await agent.resource('flowModelTemplates').create({
diff --git a/packages/plugins/@nocobase/plugin-ui-templates/src/server/plugin.ts b/packages/plugins/@nocobase/plugin-ui-templates/src/server/plugin.ts
index de436ad461f..5c37d23053e 100644
--- a/packages/plugins/@nocobase/plugin-ui-templates/src/server/plugin.ts
+++ b/packages/plugins/@nocobase/plugin-ui-templates/src/server/plugin.ts
@@ -121,23 +121,36 @@ export class PluginBlockReferenceServer extends Plugin {
       }
     };
 
-    const removeUsagesByInstance = async (
-      instanceUid: string,
-      _options: any,
-      { transaction }: { transaction?: any } = {},
-    ) => {
+    const removeUsagesByInstances = async (instanceUids: string[], { transaction }: { transaction?: any } = {}) => {
       const usageRepo = this.db.getRepository('flowModelTemplateUsages');
-      await usageRepo.destroy({ filter: { modelUid: instanceUid }, transaction });
+      const uids = _.uniq(instanceUids.map(String).filter(Boolean));
+      for (const chunk of _.chunk(uids, 500)) {
+        await usageRepo.destroy({
+          filter: {
+            modelUid: {
+              $in: chunk,
+            },
+          },
+          transaction,
+        });
+      }
     };
 
     // 区块删除时自动清理 usage 记录，避免垃圾数据
     this.db.on('flowModels.afterDestroy', async (instance: any, { transaction }: any = {}) => {
       const instanceUid = instance?.get?.('uid') || instance?.uid;
       if (!instanceUid) return;
-      const options = parseOptions(instance?.get?.('options') || instance?.options);
-      await removeUsagesByInstance(instanceUid, options, { transaction });
+      await removeUsagesByInstances([instanceUid], { transaction });
     });
 
+    this.db.on(
+      'flowModels.beforeRemoveTree',
+      async ({ uids }: { rootUid?: string; uids?: string[] } = {}, options: { transaction?: any } = {}) => {
+        if (!uids?.length) return;
+        await removeUsagesByInstances(uids, { transaction: options?.transaction });
+      },
+    );
+
     // 区块保存时维护 usage：
     // - referenceSettings.useTemplate.templateUid（且 mode!==copy）
     // - popupSettings.openView.popupTemplateUid + popupTemplateMode!==copy
@@ -201,11 +214,7 @@ export class PluginBlockReferenceServer extends Plugin {
         for (const node of nodes) {
           const instanceUid = node?.uid;
           if (!instanceUid) continue;
-          const options = parseOptions(node?.options || {});
-          if (node?.parent && !options?.parentId) {
-            options.parentId = node.parent;
-          }
-          await removeUsagesByInstance(instanceUid, options, { transaction: ctx.transaction });
+          await removeUsagesByInstances([instanceUid], { transaction: ctx.transaction });
         }
         return;
       }
diff --git a/packages/plugins/@nocobase/plugin-ui-templates/src/server/resources/flowModelTemplates.ts b/packages/plugins/@nocobase/plugin-ui-templates/src/server/resources/flowModelTemplates.ts
index cfbec9d0f92..f7365ccbc66 100644
--- a/packages/plugins/@nocobase/plugin-ui-templates/src/server/resources/flowModelTemplates.ts
+++ b/packages/plugins/@nocobase/plugin-ui-templates/src/server/resources/flowModelTemplates.ts
@@ -238,6 +238,13 @@ export default {
           data: { usageCount },
         });
       }
+      const templateRepo = ctx.db.getRepository('flowModelTemplates');
+      const template = await templateRepo.findOne({
+        filter: { uid: templateUid },
+        transaction: ctx.transaction,
+        context: ctx,
+      });
+      const targetUid = template?.get?.('targetUid') || template?.targetUid;
       await actions.destroy(ctx, next);
       // 兜底清理孤立 usage（正常情况下 usageCount 已为 0）
       await usageRepo.destroy({
@@ -246,6 +253,10 @@ export default {
         },
         context: ctx,
       });
+      if (targetUid) {
+        const flowRepo = ctx.db.getRepository('flowModels') as FlowModelRepository;
+        await flowRepo.remove(targetUid, { transaction: ctx.transaction });
+      }
     },
   },
 };