Today my server crash by luckperms with this error:
https://paste.ubuntu.com/p/HDW7RPShTT/
i'm search and found this page
https://github.com/lucko/LuckPerms/wiki/Storage-system-errors
On my server, Luckperms (Ver 4.2.2) maximum-lifetime is default (30 minutes) and Mysql wait-timeout is 43200 (12 hours) as you can see in here
mysqld --verbose --help: https://paste.ubuntu.com/p/gNf3ZXqPWV/
i'm config correctly why error still happen?
i have 6 servers run Luckperms connect to same database, but only 1 server happen this issue. Don't know why.

I'm not sure, although the error you linked wasn't the cause of the server crashing, it might be because of it crashing?

Yes, it's not crash, just disconnect all players and make players can't play.
Is connect-timeout 5 on mysql related to this issue?

today it happen again, don't know why only this server facing this issue, other (5 servers, same config) don't has this issue.

As I said,

the error you linked wasn't the cause of the server crashing, it might be because of it crashing

Most likely another plugin lagging the server, causing connections to be dropped, and the LP database pool to report a lapse in system time

I'm pretty sure this is unrelated to LuckPerms