If notch filter is inserted into magnetic and electrostatic suspension system to eliminate unbalance vibration, the stability of the system is influenced. A design method of the notch filter is put forward, which gives the consideration of the restraining of the disturbance and the stability of the system. The filter used a kind of general structure, whose central frequency located nearby the rotation speed to reduce the unbalance vibration. The other three parameters were relevant to the bandwidth and the polar distribution of the filter, which could be used to influence the stability of the system. The transfer function and the stability equation of the system with the notch filter are found, and the root locus and frequency domain method are used to find the mathematic relationship between filter parameters and system properties. Then the filter is designed, which takes margin, stiffness, amplitude and filtering effect into consideration as a whole. The experimental result shows that after using the notch filter, the speed attenuation and the voltage are reduced by 91% and 67% respectively, and the stability margin and the vibration amplitude meet the design target.