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Rotor unbalance and sensor runout are the two major interference sources in magnetically suspended flywheel (MSF), which can induce undesirable harmonic vibration and reduce the attitude control precision of spacecraft. To further suppress the harmonic vibration caused by multiple interference sources, a compound control method is proposed in this paper. Firstly, the mechanism of harmonic vibration is analyzed. The rotor unbalance mainly generates the single harmonic vibration and the sensor runout generates multiple harmonic vibration. Secondly, on the basis of the characteristics of the two kinds of interference, the generalized notch filter and the repetitive control method are adopted to suppress the harmonic vibration caused by sensor runout and rotor unbalance, respectively. Thirdly, in order to reduce the difficulty of controller design, a plug-in structure is adopted to the repetitive controller. And then the two control methods can be designed independently. The stability and the interference suppression capability of the proposed method were analyzed. Lastly, the effectiveness of the proposed method has been experimentally verified.