The mass imbalance of the rotor will produce the synchronous vibration force that is transmitted to the magnetically suspended control moment gyroscope (MSCMG) through the magnetic levitation stator, which affects the imaging performance of the satellite. The suppression of the synchronous vibration force needs the speed signal. In order to solve the synchronous vibration force of the MSCMG when the speed measurement sensor fails, this paper proposed an modified double second-order generalized integral frequency-locked loop (SOGI-FLL) method, which uses the frequency of the disturbance signal generated through the mass imbalance of the rotor to adaptively estimate the rotor speed and suppress the synchronous vibration force generated by the active magnetic bearing system. The phase compensation is introduced to ensure the stability of the system in full frequency band. The electromagnetic force is directly used as the input signal of the control algorithm to achieve zero magnetic force control. Simulation and experimental are carried out, and the results are given to prove that the algorithm proposed in this paper can accurately estimate the rotation speed and achieve the vibration force suppression in the full rotation speed range. It is of great significance for the high-precision control of the active magnetic bearing rotor system.