The magnetic damper was introduced into the high speed rotating machinery to restrain the vibration of the rotor supported by active magnetic bearings. The experimental setup, which was made up of one rotor, two radial active magnetic bearings, one axial active magnetic bearing, one magnetic damper and control system, was built to investigate the effects of the magnetic damper locations on dynamic characteristics of the system by theoretical analysis, experimental modal analysis and actual operation of the system. The results show that the vibration of the active magnetic bearing system operating at the modal frequency can be reduced more effectively if the magnetic damper is located far from the nodes of the corresponding mode shape.