The present disclosure provides a photomask inspection system and an inspection method. The mask inspection system includes: a mask thickness measuring device having sensor modules arranged side by side for measuring the thickness of the mask; a bar code reading device; a calibration device including a calibration rod and an electromagnet, the calibration rod includes a calibration stick and a calibration base, the electromagnet is set at the bottom of the calibration base, and the calibration device calibrates the barcode reading device.