Abstract: Active magnetic bearing (AMB) is usually used as the supporting structure of high-speed flywheel energy storage system. Proportional–derivative controller (PD controller) is widely applied to the vibration control of the active magnetic bearing flywheel rotor system. In the conventional PD controller, the damping control signals are calculated by the derivative of rotor displacement signals, however, the differential operation may result in noise interference. The control system cannot be damped adequately due to the influence of noise interference, which makes the performances of vibration control of the flywheel rotor system become worse and may lead to system instability. For this problem, a novelty PD control strategy based on velocity observer is proposed. In the control strategy, the damping control signals are calculated by a velocity observer to improve the ability of against noise. Firstly, the basic principle of the novelty control strategy proposed is described. Then the performances of novelty control system are validated by simulations and experiments, respectively. The results show that, compared to the conventional PD control method, the novelty PD control strategy proposed has better ability of against noise and larger stability region.