When the rotor of active magnetic bearing (AMB) systems rotates at high-speed, periodic vibration response can be generated in the systems, which can reduce system control precision, stability and limit the rotor speed, etc. For the vibration response in the systems, firstly, the causes of periodic vibration are analyzed from the Mechanical properties of rotor and the process of control system; secondly, the sinusoidal signal of vibration embodied in the system control process is treated as an objective, and PID controller combined with least mean square (LMS) algorithm is adopted to adaptive filter thirdly, by analyseing the fixed step size LMS algorithm, the PID parameters and the frequency interaction of the signals, one real-time switching compensation control strategy according to the frequency is presented. The effectiveness of the method is demonstrated through experiments, which the foundation for the speed increase of AMB system.