A method of measuring a center error between bearings includes disposing both sides of a rotation shaft on inner circumferential surfaces of a magnetic bearing and a backup bearing, applying current to the magnetic bearing to produce movement of the rotation shaft, determining a contact point between the rotation shaft and the backup bearing according to movement of the rotation shaft, determining a final target value using the contact point and predetermined position information of the magnetic bearing, determining a magnetic center of the magnetic bearing through the final target value, comparing the magnetic center of the magnetic bearing and a mechanical center of the backup bearing to determine a center error, and aligning the magnetic center of the magnetic bearing and the mechanical center of the backup bearing based on the determined center error.