In a maglev flywheel system, an unbalanced interference signal synchronous with the flywheel frequency will be produced because the flywheel rotor is uneven. This signal can reduce system control precision and stability, and make the system produce unbalance force vibration. Therefore, the signal should be filtered to reduce the effects on the control system. A vibration switching compensation control strategy is proposed based on the standard least mean squares (LMS) algorithm and one proportional–integral–derivative (PID) controller. The flywheel's rotational frequency is measured in real time as the switching reference, and different LMS algorithm step sizes and different PID controller parameters are adopted in different rotational frequencies. Simulation and experimental results verify the feasibility and effectiveness of the switch compensation strategy, which can reduce the control current amplitude and make the flywheel rotate around the inertial principal axis as much as possible. © 2018 Institute of Electrical Engineers of Japan. Published by John Wiley & Sons, Inc.