Aiming at the High Energy Photon Source which needs to calibrate the center of a large number of magnets, a scheme of calibrating the center of magnetic machinery based on coordinate measuring machine (CMM) is proposed, the process and method of writing automatic measuring program are determined, and the calibration of various types of magnets in the accelerator is completed. The results show that the calibration repeatability of the reference point of collimation is within 0.01 mm by calibrating the mechanical center twice for each magnet. The standard deviation between the measured value and the design value is within 0.015 mm. The calibration efficiency is 2 times higher than that of the laser tracker. This method of magnet calibration with CMM can improve the calibration accuracy, reduce the labor cost, improve the work efficiency, provide reference for the magnet center extraction calibration in the accelerator work, ensure the smooth installation of the accelerator device, and meet the requirements of the accelerator alignment measurement project schedule.