Then I learn that there're default menu configuration somewhere. One of them is at /etc/xdg/menu which there're applications.menu and settings.menu for application menu and system setting menu respectively. And each user has its own customization of menu in ~/.config/menus which has applications.menu and settings.menu too. Those files contain some exclude configurations and they are merged with default configurations when it is used. So deleting directory ~/.config/menus should reset the main menu to default state and that's all.
rm -rf ~/.config/menus
and logout and login again.
but if it's still not be reset like in my case, it need to delete *.desktop in your home directory too.
find ~/ -name "*.desktop" -delete