In modern industries, high-speed motors and generators have received great attention, and they are widely used in micro turbine, centrifugal compressor, blower, etc. However, the resonance vibration of flexible rotor will become a challenging issue when the rotor has to operate above the first bending critical speed. In this paper, a phase compensation method is proposed to improve the damping level of the flexible rotor around the first bending critical speed. The dynamic characteristics of the flexible rotor are analyzed, and the modal frequency is obtained. The rotor finite element model is verified by the modal test. Based on Proportion-Integration-Differentiation (PID) controller, the phase of the control system is shaped with different general filters to improve the damping level of the flexible rotor around the first bending critical speed. The simulation and experimental results indicate that the first bending mode damping of rotor is obviously enhanced by phase compensation. The phase compensation method can effectively suppress the resonance vibration of the rotor and make the rotor smoothly pass the first bending critical speed, achieving supercritical operation.