Hi Kaiyin. I'm Greg, awarded MVP for eleven years, Volunteer Moderator, and Independent Advisor here to help you until this is resolved.
We see a lot of reports about Storage Usage settings misreporting files by a huge amount. Recently I've begun to see the same for File Explorer.
I see your ran WinDirStat. To cross-check this you can install TreeSize to get a visual picture of what's eating up drive space. See how here:
https://www.groovypost.com/howto/map-hardrive-u.... If they agree I would trust them most.
Run a full Disk Check to check over the file system: https://www.groovypost.com/howto/check-hard-dri...
Run a full scan with the most powerful on-demand free scanner Malwarebytes:
https://www.malwarebytes.com/mwb-download/.
In the Scan Settings first set it to include scanning for Rootkits.
If necessary run it in Safe Mode with Networking, or Safe Mode accessed by one of these methods: https://www.digitalcitizen.life/4-ways-boot-saf...
Clean up anything found, restart PC and then run again until it comes up clean.
Then run a full scan with AdwCleaner from http://www.bleepingcomputer.com/download/adwcle.... Clean Up anything found.
Check for any remainders in Settings > Apps > Apps & Features, and also in each of your browser's Extensions, Home Page settings, Search service or Add-On's as shown here: https://community.box.com/t5/How-to-Guides-for-...
Then check for damaged System Files: https://www.lifewire.com/how-to-use-sfc-scannow...
If it cannot repair them see Step 10 here to continue: http://answers.microsoft.com/en-us/windows/wiki...
If these don't fix it continue with the rest of the steps in the checklist in link just above.
If nothing else works then do a Repair Install, by installing Media Creation Tool and then choosing to Upgrade Now. This reinstalls Windows while keeping files, programs and most settings in place, and is also the most stable method to advance to the latest version. http://windows.microsoft.com/en-us/windows-10/m...
If you want to keep Malwarebytes as an on-demand scanner then you can turn off its Real Time trial version in it's Settings > Account Details tab.
I hope this helps. Feel free to ask back any questions and keep me posted. If you will wait to choose if I solved your problem, I will keep working with you until it's resolved.
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