Membership High MySQL Usage

Have about 3k members registered on website with membership with different membership status like active, expired.

Membership 2 Pro has a Cron function for check membership status at every 6hours. Now issue is that it checks each and every user's membership status, and update membership accordingly so this cause a huge Mysql query, and brings the server down, every 6 hours.

Don't see any specific log, or server error related to this. But could notice high server load every six hours.
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Would like to know any workaround to to fix how the cron checks, or anything helpful.