The rated rotational speed of the magnetically suspended motor (MSM) is always above the bending critical speed to achieve high energy density. The rotor will have a dramatic resonance when it passes the critical speed. Then, the magnetic bearing has to provide large bearing force to suppress the synchronous vibration. However, the bearing force is always limited by magnetic saturation and power amplifier voltage saturation. This paper proposed an optimum damping control method which can make effective use of the limited bearing force to minimize the synchronous vibration amplitude of the rotor nearby the critical speed. The accurate rotor model is obtained by theoretical analysis and system identification. The unbalance force response of the bending mode of the rotor is analyzed. The small gain theorem is used to determine the range of the magnitude of the control system. Then, the relationship of the optimum damping varying with the magnitude and phase of the control system nearby the critical speed is analyzed. The run-up experiments are carried out in 315 kW MSM and the results show the effectiveness and superiority of the optimum damping control method.