diff --git a/src/Router.php b/src/Router.php
index 04fba0a..aa5927c 100644
--- a/src/Router.php
+++ b/src/Router.php
@@ -312,9 +312,28 @@ class Router
 		);
 		$scanner->setConfig($scanConfig);
 
+		// 从 manifest 获取 Master 扫描过的类
 		$manifestEntries = $scanner->getManifestClasses();
-		if (empty($manifestEntries)) {
-			\Kiri::getLogger()->warning('Annotation route rebuild: manifest is empty, annotation routes will NOT be registered');
+		$manifestClasses = [];
+		foreach ($manifestEntries as $entry) {
+			if (is_array($entry) && isset($entry['classes'])) {
+				foreach ($entry['classes'] as $c) {
+					$manifestClasses[$c] = true;
+				}
+			}
+		}
+
+		// 关键：manifest 只包含 Scanner 通过 require_once 新发现的类
+		// 但路由文件加载时 $container->get(Controller) 会触发 autoload 提前加载类
+		// 导致 Scanner 的 require_once 变成 no-op，该类及其注解永久丢失
+		// 因此必须合并 get_declared_classes() 补扫所有已声明的用户空间类
+		$allDeclared = get_declared_classes();
+		foreach ($allDeclared as $class) {
+			$manifestClasses[$class] = true;
+		}
+
+		if (empty($manifestClasses)) {
+			\Kiri::getLogger()->warning('Annotation route rebuild: no classes to process');
 			return;
 		}
 
@@ -323,84 +342,93 @@ class Router
 		$errorCount    = 0;
 		$dispatchCount = 0;
 
-		foreach ($manifestEntries as $path => $entry) {
-			$classes = is_array($entry) && isset($entry['classes']) ? $entry['classes'] : [];
-			foreach ($classes as $class) {
-				if (!class_exists($class)) {
+		// 只处理用户命名空间下的类，排除框架和 PHP 内置类
+		$userNamespaces = $scanConfig['user_namespaces'] ?? ['App\\'];
+
+		foreach (array_keys($manifestClasses) as $class) {
+			$isUserClass = false;
+			foreach ($userNamespaces as $ns) {
+				if (str_starts_with($class, $ns)) {
+					$isUserClass = true;
+					break;
+				}
+			}
+			if (!$isUserClass) {
+				continue;
+			}
+			if (!class_exists($class)) {
+				continue;
+			}
+			$classCount++;
+			try {
+				$reflect = $container->getReflectionClass($class);
+				if (!$reflect->isInstantiable() || $reflect->isTrait() || $reflect->isEnum() || $reflect->isInterface() || $reflect->isAbstract()) {
 					continue;
 				}
-				$classCount++;
-				try {
-					$reflect = $container->getReflectionClass($class);
-					if (!$reflect->isInstantiable() || $reflect->isTrait() || $reflect->isEnum() || $reflect->isInterface()) {
+				foreach ($reflect->getMethods() as $method) {
+					if ($method->isStatic() || $method->getDeclaringClass()->getName() !== $class) {
 						continue;
 					}
-					foreach ($reflect->getMethods() as $method) {
-						if ($method->isStatic() || $method->getDeclaringClass()->getName() !== $class) {
+					foreach ($method->getAttributes() as $attribute) {
+						$attrName = $attribute->getName();
+						if (!class_exists($attrName)) {
 							continue;
 						}
-						foreach ($method->getAttributes() as $attribute) {
-							$attrName = $attribute->getName();
-							if (!class_exists($attrName)) {
-								continue;
-							}
-							try {
-								$instance = $attribute->newInstance();
-								if ($instance instanceof Kiri\Di\Interface\InjectMethodInterface) {
-									$instance->dispatch($class, $method->getName());
-									$dispatchCount++;
-								}
-							} catch (\Throwable $e) {
-								$errorCount++;
-								\Kiri::getLogger()->error("Annotation rebuild error [{$class}::{$method->getName()} @ {$attrName}]: {$e->getMessage()}");
+						try {
+							$instance = $attribute->newInstance();
+							if ($instance instanceof Kiri\Di\Interface\InjectMethodInterface) {
+								$instance->dispatch($class, $method->getName());
+								$dispatchCount++;
 							}
+						} catch (\Throwable $e) {
+							$errorCount++;
+							\Kiri::getLogger()->error("Annotation rebuild error [{$class}::{$method->getName()} @ {$attrName}]: {$e->getMessage()}");
 						}
 					}
-				} catch (\Throwable $e) {
-					$errorCount++;
-					\Kiri::getLogger()->error("Annotation rebuild class [{$class}]: {$e->getMessage()}");
 				}
+			} catch (\Throwable $e) {
+				$errorCount++;
+				\Kiri::getLogger()->error("Annotation rebuild class [{$class}]: {$e->getMessage()}");
 			}
 		}
 
 		$router = $container->get(DataGrip::class)->get(static::$type);
 		$routeCount = count($router->dump());
 
-		\Kiri::getLogger()->info("Annotation route rebuild: {$classCount} classes processed, {$dispatchCount} annotation routes dispatched, {$routeCount} total routes, {$errorCount} errors");
+		\Kiri::getLogger()->info("Annotation route rebuild: {$classCount} user classes processed, {$dispatchCount} annotation routes dispatched, {$routeCount} total routes, {$errorCount} errors");
 
-		// 搜索特定路径的诊断日志，方便排查 404 问题
+		// 搜索特定路径的诊断日志
 		$searchPaths = ['/headers'];
 		foreach ($searchPaths as $searchPath) {
 			$found = [];
-			foreach ($manifestEntries as $path => $entry) {
-				$classes = is_array($entry) && isset($entry['classes']) ? $entry['classes'] : [];
-				foreach ($classes as $class) {
-					try {
-						$reflect = $container->getReflectionClass($class);
-						foreach ($reflect->getMethods() as $method) {
-							foreach ($method->getAttributes() as $attr) {
-								if (in_array($attr->getName(), [
-									\Kiri\Router\Annotate\Get::class,
-									\Kiri\Router\Annotate\Post::class,
-									\Kiri\Router\Annotate\Put::class,
-									\Kiri\Router\Annotate\Delete::class,
-									\Kiri\Router\Annotate\Route::class,
-								])) {
-									$instance = $attr->newInstance();
-									$routePath = $instance->path ?? '';
-									if (str_contains($routePath, 'header')) {
-										$found[] = "{$class}::{$method->getName()} -> {$attr->getName()} path={$routePath} version={$instance->version}";
-									}
+			foreach (array_keys($manifestClasses) as $class) {
+				if (!class_exists($class)) continue;
+				try {
+					$reflect = $container->getReflectionClass($class);
+					foreach ($reflect->getMethods() as $method) {
+						foreach ($method->getAttributes() as $attr) {
+							if (in_array($attr->getName(), [
+								\Kiri\Router\Annotate\Get::class,
+								\Kiri\Router\Annotate\Post::class,
+								\Kiri\Router\Annotate\Put::class,
+								\Kiri\Router\Annotate\Delete::class,
+								\Kiri\Router\Annotate\Route::class,
+							])) {
+								$instance = $attr->newInstance();
+								$routePath = $instance->path ?? '';
+								if (str_contains($routePath, 'header')) {
+									$version = $instance->version ?? '';
+									$found[] = "{$class}::{$method->getName()} path={$routePath} version={$version}";
 								}
 							}
 						}
-					} catch (\Throwable) {}
-				}
+					}
+				} catch (\Throwable) {}
 			}
 			if (!empty($found)) {
 				\Kiri::getLogger()->info("Annotation route search '{$searchPath}': " . implode(' | ', $found));
 			} else {
-				\Kiri::getLogger()->warning("Annotation route search '{$searchPath}': NO annotation found in any of {$classCount} classes");
+				\Kiri::getLogger()->warning("Annotation route search '{$searchPath}': NO annotation found in any class");
 			}
 		}
 	}