My list has 5129 items but I have increased threshold limit up to 5 lac in SharePoint on-prem environment. When a normal user tries to apply a filter to the list the loads very slow. But it not happening using system account. It option loads fast using system account. Also, there are only 10 options in the filter
Are you using item level permissions on the list?
A System account will bypass permission checks on a list and that could explain the performance gain. Otherwise, get a fiddler trace and check where the time is wasted...
Also you could consider indexing the field in question for a better performance... The filter has no clue that there are only 10 items available.
You can narrow down this issue as the following:
clear the browser cache.
Clear SharePoint Configuration cache.