As rotor imbalance can lead to the synchronous disturbances of Magnetically Suspended Control Moment Gyroscopes (MSCMG), and can reduce the attitude control accuracy and the load accuracy of spacecrafts, A general control strategy based on a sliding mode disturbance observer was proposed to minimize the synchronous vibration caused by unbalance on a rotor. First, a dynamics model of the magnetic bearing-rotor system was set up and the sliding mode observer used for disturbance observation was designed. Then, a Tracking Differentiator (TD) was used to estimate the differential signals from a displacement sensor to obtain the velocity signals and to reduce orders of the observer. Finally, according to the synchronous force estimated by the disturbance observer, a controller was designed to compensate the vibration caused by unbalance of the rotor. Simulation and experimental results demonstrate the effectiveness of the proposed approach and the vibration has been decreased by 72%.