Synchronous vibration, a common issue in active magnetic bearing (AMB) system, is mainly caused by mass imbalance of the rotor. It comes with high-power consumption and serious impact on the housing base, dramatically degrading the performance of AMB. Magnetically suspended flywheel (MSFW), which owns a flat rotor and consequently shows strong gyroscopic effects even at low operating speed, requires additional attention not only for suppressing the synchronous vibration but also for maintaining the overall stability faced with the coupled dynamics. In this work, in order to suppress the vibration torques in MSFW with significant gyroscopic effects, an improved synchronous rotating frame- (SRF-) based control method is proposed. The proposed method introduces the compensation phase for stability adjustment and aims at simultaneously suppressing the synchronous components in the coupled axes. Firstly, the vibration torque model of MSFW is established, and the baseline control strategy for suspension and gyroscopic effects restrain is derived. Then, the principle and implementation of the improved SRF-based vibration torque method are analyzed, which aims at suppressing the synchronous vibration torques through attenuating synchronous components in coil currents. Moreover, the stability of the overall closed-loop system is analyzed. Finally, the effectiveness of the proposed method is verified through simulation and experimental results.