When I switch the windows to windows using Alt+Tab, and back to Minecraft, the config GUI and all the hotkeys I set have no response.

Your Alt key is probably stuck, does it get fixed if you press it once after switching back to Minecraft?

After wait for a day for it happens again, I found that press ALT does not help anything, instead it can be fixed by switching out and in to Minecraft again

Then could you also try the things outlined here: maruohon/malilib#16 (comment)

I have had that issue before and not just with tweakeroo but also litematica, pretty sure its a fabric bug