Assuming there is some commonality between the users you want to delete, you might look at the answers to this question: Delete all subscribers from wp_users and wp_usermeta a few thousand at a time
Make sure you have a backup of your database, though, as an error in the selection of the users could delete important users (like admins). If you are going to go this route, test the sql statement first to ensure you didn’t select a critical user, or one that you really don’t want to delete.
In fact, I’d copy the WP database, and then ‘practice’ on that database.