The Maglev motor has the characteristics of high-speed and high-power density, and is widely used in compressors, molecular pumps and other high-speed rotating machinery. With the requirements of miniaturization and high speed of rotating machinery, the rotor of the maglev motor will operate above the bending critical speed, and the critical vibration control of the flexible rotor is facing challenges. In order to solve the problem of the critical vibration suppression of the maglev high-speed motor, the system model of the maglev motor is established, the rotordynamics of the flexible rotor are analyzed and the rotor model is modal truncated to reduce the order. Then, the μ–controller is designed, and the weighting functions are designed to deal with the modal uncertainty. Finally, an experimental platform of the maglev motor with the flexible rotor is built to verify the effect of the μ–control on the suppression of the critical vibration of the maglev rotor.