diff --git a/apps/ll-package-manager/src/main.cpp b/apps/ll-package-manager/src/main.cpp
index 26137f8a6..f50da7939 100644
--- a/apps/ll-package-manager/src/main.cpp
+++ b/apps/ll-package-manager/src/main.cpp
@@ -11,7 +11,6 @@
 #include "linglong/repo/ostree_repo.h"
 #include "linglong/utils/configure.h"
 #include "linglong/utils/dbus/register.h"
-#include "linglong/utils/file.h"
 #include "linglong/utils/global/initialize.h"
 #include "ocppi/cli/CLI.hpp"
 #include "ocppi/cli/crun/Crun.hpp"
@@ -51,23 +50,9 @@ void withDBusDaemon(ocppi::cli::CLI &cli)
     }
     auto *ostreeRepo = new linglong::repo::OSTreeRepo(repoRoot, *config, *clientFactory);
     ostreeRepo->setParent(QCoreApplication::instance());
-    {
-        auto exportVersion = repoRoot.absoluteFilePath("entries/.version").toStdString();
-        auto data = linglong::utils::readFile(exportVersion);
-        if (data && data == LINGLONG_EXPORT_VERSION) {
-            qDebug() << exportVersion.c_str() << data->c_str();
-            qDebug() << "skip export entry, already exported";
-        } else {
-            auto ret = ostreeRepo->exportAllEntries();
-            if (!ret.has_value()) {
-                qCritical() << "failed to export entries:" << ret.error();
-            } else {
-                ret = linglong::utils::writeFile(exportVersion, LINGLONG_EXPORT_VERSION);
-                if (!ret.has_value()) {
-                    qCritical() << "failed to write export version:" << ret.error();
-                }
-            }
-        }
+    auto result = ostreeRepo->fixExportAllEntries();
+    if (!result.has_value()) {
+        qCritical() << result.error().message();
     }
 
     auto *containerBuilder = new linglong::runtime::ContainerBuilder(cli);
@@ -78,7 +63,7 @@ void withDBusDaemon(ocppi::cli::CLI &cli)
                                                                  *containerBuilder,
                                                                  QCoreApplication::instance());
     new linglong::adaptors::package_manger::PackageManager1(packageManager);
-    auto result = registerDBusObject(conn, "/org/deepin/linglong/PackageManager1", packageManager);
+    result = registerDBusObject(conn, "/org/deepin/linglong/PackageManager1", packageManager);
     if (!result.has_value()) {
         qCritical().noquote() << "Launching failed:" << Qt::endl << result.error().message();
         QCoreApplication::exit(-1);
@@ -126,6 +111,10 @@ void withoutDBusDaemon(ocppi::cli::CLI &cli)
 
     auto *ostreeRepo = new linglong::repo::OSTreeRepo(repoRoot, *config, *clientFactory);
     ostreeRepo->setParent(QCoreApplication::instance());
+    auto result = ostreeRepo->fixExportAllEntries();
+    if (!result.has_value()) {
+        qCritical() << result.error().message();
+    }
 
     auto *containerBuilder = new linglong::runtime::ContainerBuilder(cli);
     containerBuilder->setParent(QCoreApplication::instance());
diff --git a/libs/linglong/src/linglong/repo/ostree_repo.cpp b/libs/linglong/src/linglong/repo/ostree_repo.cpp
index 9ffea0ddb..11ee13a42 100644
--- a/libs/linglong/src/linglong/repo/ostree_repo.cpp
+++ b/libs/linglong/src/linglong/repo/ostree_repo.cpp
@@ -18,6 +18,7 @@
 #include "linglong/repo/config.h"
 #include "linglong/utils/command/env.h"
 #include "linglong/utils/error/error.h"
+#include "linglong/utils/file.h"
 #include "linglong/utils/finally/finally.h"
 #include "linglong/utils/gkeyfile_wrapper.h"
 #include "linglong/utils/packageinfo_handler.h"
@@ -1640,8 +1641,37 @@ utils::error::Result<void> OSTreeRepo::exportDir(const std::string &appID,
                     return LINGLONG_ERR("remove file failed", ec);
                 }
             }
-            auto ret = IniLikeFileRewrite(QFileInfo(source_path.c_str()), appID.c_str());
-            if (!ret) { }
+
+            {
+                auto info = QFileInfo(target_path.c_str());
+                if ((info.path().contains("share/applications") && info.suffix() == "desktop")
+                    || (info.path().contains("share/dbus-1") && info.suffix() == "service")
+                    || (info.path().contains("share/systemd/user") && info.suffix() == "service")
+                    || (info.path().contains("share/applications/context-menus"))) {
+                    // We should not modify the files of the checked application directly, but
+                    // should copy them to root entries directory and then modify.
+                    std::filesystem::copy(source_path, target_path, ec);
+                    if (ec) {
+                        return LINGLONG_ERR("copy file failed: " + target_path.string(), ec);
+                    }
+
+                    exists = std::filesystem::exists(target_path, ec);
+                    if (ec) {
+                        return LINGLONG_ERR("check file exists", ec);
+                    }
+
+                    if (!exists) {
+                        qWarning() << "failed to copy file: " << source_path.c_str();
+                        continue;
+                    }
+
+                    auto ret = IniLikeFileRewrite(QFileInfo(target_path.c_str()), appID.c_str());
+                    if (ret) {
+                        continue;
+                    }
+                }
+            }
+
             std::filesystem::create_symlink(source_path, target_path, ec);
             if (ec) {
                 return LINGLONG_ERR("create symlink failed: " + target_path.string(), ec);
@@ -1735,6 +1765,30 @@ OSTreeRepo::exportEntries(const std::filesystem::path &rootEntriesDir,
     return LINGLONG_OK;
 }
 
+utils::error::Result<void> OSTreeRepo::fixExportAllEntries() noexcept
+{
+    auto exportVersion = repoDir.absoluteFilePath("entries/.version").toStdString();
+    auto data = linglong::utils::readFile(exportVersion);
+    if (data && data == LINGLONG_EXPORT_VERSION) {
+        qDebug() << exportVersion.c_str() << data->c_str();
+        qDebug() << "skip export entry, already exported";
+    } else {
+        auto ret = exportAllEntries();
+        if (!ret.has_value()) {
+            qCritical() << "failed to export entries:" << ret.error();
+            return ret;
+        } else {
+            ret = linglong::utils::writeFile(exportVersion, LINGLONG_EXPORT_VERSION);
+            if (!ret.has_value()) {
+                qCritical() << "failed to write export version:" << ret.error();
+                return ret;
+            }
+        }
+    }
+
+    return LINGLONG_OK;
+}
+
 utils::error::Result<void> OSTreeRepo::exportAllEntries() noexcept
 {
     LINGLONG_TRACE("export all entries");
diff --git a/libs/linglong/src/linglong/repo/ostree_repo.h b/libs/linglong/src/linglong/repo/ostree_repo.h
index 392198891..a7a40bafe 100644
--- a/libs/linglong/src/linglong/repo/ostree_repo.h
+++ b/libs/linglong/src/linglong/repo/ostree_repo.h
@@ -90,8 +90,6 @@ class OSTreeRepo : public QObject
     utils::error::Result<void> prune();
 
     void removeDanglingXDGIntergation() noexcept;
-    // exportEntries will clear the entries/share and export all applications to the entries/share
-    utils::error::Result<void> exportAllEntries() noexcept;
     // exportReference should be called when LayerDir of ref is existed in local repo
     void exportReference(const package::Reference &ref) noexcept;
     // unexportReference should be called when LayerDir of ref is existed in local repo
@@ -121,6 +119,7 @@ class OSTreeRepo : public QObject
     getLayerItem(const package::Reference &ref,
                  std::string module = "binary",
                  const std::optional<std::string> &subRef = std::nullopt) const noexcept;
+    utils::error::Result<void> fixExportAllEntries() noexcept;
 
 private:
     api::types::v1::RepoConfig cfg;
@@ -164,6 +163,8 @@ class OSTreeRepo : public QObject
                                          const std::filesystem::path &source,
                                          const std::filesystem::path &destination,
                                          const int &max_depth);
+    // exportEntries will clear the entries/share and export all applications to the entries/share
+    utils::error::Result<void> exportAllEntries() noexcept;
 };
 
 } // namespace linglong::repo