The resonance vibration control of flexible rotor supported on active magnetic bearings (AMB) is a challenging issue in the industrial applications. This work addresses the application of robust control method to the resonance vibration control for AMB flexible rotor while passing through the critical speed. This model-based method shows great superiority to handling flexible mode vibration, which can guarantee robust stability and performance when encountering modal perturbation. First, the designed flexible rotor-AMB test rig is briefly introduced. Then the system modeling is described in detail including flexible rotor, power amplifier, displacement sensors and magnetic actuator and rotordynamics are analyzed. Model validation is carried out by sine sweeping test. Finally, the -synthesis controller is designed. The simulation and experimental results indicate that the designed -synthesis controller, which shows great robustness to modal perturbation, can effectively suppress the resonance vibration of flexible rotor and achieve supercritical operation.