Magnetic Suspension Flywheel (MSFW) is regarded as a promising attitude control actuator for the ultra-precision and long life-span spacecraft. The output vibration of an operating MSFW is an important criterion to evaluate the system’s performance. Based on the dynamics model of rotor with the residual imbalances and the transfer functions of the controller, the restoring electromagnetic forces and torques for the suspension of the rotor is calculated. Then a testing rig was designed to measure the displacements, currents and vibration outputs of the MSFW. The vibrations of the basement caused by reactions of the restoring forces and torques are calculated. In the end, the displacements, currents and vibrations of the operating MSFW are measured to evaluate the performance of the MSFW.