Photos library file size exceeds disk capacity

The Finder is not always calculating the file size of the Photos Library correctly.

The Photos Library is a package of many files and folders, and the Finder is not always updating the file size of the package immediately, when the internal files are changing. You may want to check the date when the library has last been changed in the Finder. Usually restarting the Mac will make the Finder update the size of the Package.

There are many auxiliary files in the Photos Library package, that are duplicated as clones or hard links (depending on the system version and the file system format of the internal drive of your Mac) and sharing the disk blocks with the original files, but the Finder may be counting the storage of the clones and hard links as additionally used storage. Can you update to a more recent system version?

It's clear the something is wonkers with the system. Give this a try to straighten out the kinks: boot into Safe Mode according to How to use safe mode on your Mac and test to see if the problem persists. Reboot normally and test again.

NOTE 1: Safe Mode boot can take up to 3 - 5 minutes as it's doing the following; 

• Verifies your startup disk and attempts to repair directory issues, if needed

• Loads only required kernel extensions (prevents 3rd party kernel/extensions from loading)

• Prevents Startup Items and Login Items from opening automatically

• Disables user-installed fonts 

• Deletes font caches, kernel cache, and other system cache files

NOTE 2: if you have a wireless keyboard with rechargeable batteries connect it with its charging cable before booting into Safe Mode. This makes it act as a wired keyboard as will insure a successful boot into Safe Mode.

sumengshen wrote: …there’s clearly something wrong.

This is not clear to me. My question was about what problem you are seeing in the operation of the Photos app.

If you are just asking about how the APFS files system works, then check out the Wikipedia article-- Go to APFS and scan down to "Clones." Sometimes the file information reports what you would see with an older file system format, even though APFS is more efficient. I haven't seen any sort of glitching in Photos because of this.

sumengshen wrote: … what’s wrong and how may I fix it?

What exact problem are you having with Photos' operations?

What is your storage on this Mac? At System Settings>General> Storage, my Mac says 745 GB of 1TBB used. What does yours say? Is your  free storage on your Mac less than 10%?