diff --git a/packages/editor-app/src/App.tsx b/packages/editor-app/src/App.tsx
index 29bf6c0a..b1dfc369 100644
--- a/packages/editor-app/src/App.tsx
+++ b/packages/editor-app/src/App.tsx
@@ -631,6 +631,13 @@ function App() {
             await pluginLoader.unloadProjectPlugins(pluginManager);
         }
 
+        // 清理场景（会清理所有实体和系统）
+        // Clear scene (clears all entities and systems)
+        const scene = Core.scene;
+        if (scene) {
+            scene.end();
+        }
+
         // 清理模块系统
         const engineService = EngineService.getInstance();
         engineService.clearModuleSystems();
diff --git a/packages/editor-app/src/hooks/useEngine.ts b/packages/editor-app/src/hooks/useEngine.ts
index 5b67bd68..13bc3f2a 100644
--- a/packages/editor-app/src/hooks/useEngine.ts
+++ b/packages/editor-app/src/hooks/useEngine.ts
@@ -14,6 +14,15 @@ import { EditorEngineSync } from '../services/EditorEngineSync';
 let engineInitialized = false;
 let engineInitializing = false;
 
+/**
+ * 重置引擎初始化状态（在项目关闭时调用）
+ * Reset engine initialization state (called when project is closed)
+ */
+export function resetEngineState(): void {
+    engineInitialized = false;
+    engineInitializing = false;
+}
+
 export interface EngineState {
     initialized: boolean;
     running: boolean;
diff --git a/packages/editor-app/src/services/EngineService.ts b/packages/editor-app/src/services/EngineService.ts
index c89273d5..ec173cd8 100644
--- a/packages/editor-app/src/services/EngineService.ts
+++ b/packages/editor-app/src/services/EngineService.ts
@@ -28,6 +28,7 @@ import {
     type GameRuntimeConfig
 } from '@esengine/runtime-core';
 import { getMaterialManager } from '@esengine/material-system';
+import { resetEngineState } from '../hooks/useEngine';
 import { convertFileSrc } from '@tauri-apps/api/core';
 import { IdGenerator } from '../utils/idGenerator';
 import { TauriAssetReader } from './TauriAssetReader';
@@ -245,7 +246,14 @@ export class EngineService {
             ctx.uiInputSystem.unbind?.();
         }
 
+        // 清理 viewport | Clear viewport
+        this.unregisterViewport('editor-viewport');
+
+        // 重置 useEngine 的模块级状态 | Reset useEngine module-level state
+        resetEngineState();
+
         this._modulesInitialized = false;
+        this._initialized = false;
     }
 
     /**
diff --git a/packages/editor-core/src/Plugin/PluginManager.ts b/packages/editor-core/src/Plugin/PluginManager.ts
index 5211c243..7d316ae7 100644
--- a/packages/editor-core/src/Plugin/PluginManager.ts
+++ b/packages/editor-core/src/Plugin/PluginManager.ts
@@ -1159,6 +1159,11 @@ export class PluginManager implements IService {
                 }
             }
         }
+
+        // 重置初始化状态，允许下次重新初始化运行时
+        // Reset initialized flag to allow re-initialization
+        this.initialized = false;
+        logger.debug('Scene systems cleared, runtime can be re-initialized');
     }
 
     /**