Automatically rotate mongo logs in mongod.conf file
If you are using *nix system, you have few choices. You can use logrotate service and send SIGUSR1 signal to mongod/mongos process. Or you can change your config systemLog.logRotate: rename and again send SIGUSR1.

To rotate log you can give command db.adminCommand( { logRotate : 1 } ) too.

How you do it on the windows side, that I don't know.