The antminer is standalone machine with integrated controll-unit. So you must connect to the device (s3) and create this cron job ON the antminer S3.
so the procedure is:
1) ssh into antminer s3
2) create cronjob to start/stop the cgminer process or the controlling process with desired times
some resources with more info for ssh-connection and config:
https://bitcointalksearch.org/topic/setup-troubleshoot-bitmain-antminer-s3-440ghs-miner-697474
https://bitcointalksearch.org/topic/bitmain-antminer-s3-support-and-overclocking-thread-699064
https://bitcointalksearch.org/topic/guide-dogies-comprehensive-bitmain-antminer-s3-setup-hd-702653