To suppress the imbalance force in magnetically suspended rotor systems, an autobalancing control strategy based on a plural phase-shift notch filter and feedforward control method was proposed. The structure and working principle of a suspended rotor system were introduce, and a model of the magnetically suspended rotor system with rotor imbalance was described. The electrical characteristic of the imbalance force was analyzed. Then, the condition to suppress the imbalance force was calculated and the result shows that the suppression errors are mainly caused by the amplitude error and phase error from power amplifiers. By transforming the two degrees-of-freedom translational motions into a single degree-of-freedom plural equation, a plural phase-shift notch filter was proposed. Its math equations were formulated, and the notch features of the amplitude and phase were discussed. Finally, the proposed strategy was tested and verified on a magnetically suspended control moment gyro test platform. The experimental results indicate that the imbalance force has been suppressed by 94.2% with the proposed strategy, which verifies the effectiveness of the proposed control strategy. Moreover, the proposed control strategy is characterized by smooth dynamic processing and a light computational load.