Harmonic vibrations caused by rotor mass imbalance and sensor runout， the main disturbances in magnetically suspended rotor systems. To suppress these disturbances， a compound control method based on repetitive control and variable phase adaptive notch filter feedback was proposed. Firstly， by establishing a model of the magnetic suspended rotor system， the generation mechanism of different disturbing vibration forces was analyzed. Then， taking the X-direction as an example for analysis， an inserted repetitive controller was designed to suppress the harmonic vibration caused by sensor runout. An adaptive notch filter was used to extract the synchronous signal online to adaptively compensate imbalance. The stability of the system was maintained by varying the phase angle at different frequencies， and to compensate the same-frequency displacement stiffness， so that the system can effectively suppress the harmonic vibration. Finally， the proposed control method was verified by simulation and experiment. The experimental results show that the first， third and fifth harmonic vibrations are reduced by 94.4%， 90.4% and 85.9%， respectively. The harmonic vibrations can be effectively suppressed using the proposed composite control method， whose effectiveness well verified.