For the unbalance vibration of an active-passive hybrid magnetically suspended rotor caused by high speed rotation, an adaptive control method based on a sliding mode observer and a notch filter was proposed to improve the pointing accuracy and stability of attitude control for a spacecraft. The sliding mode observer was adapted to eliminate the effects of rigidity parameter perturbation and magnetic force coupling of the magnetic bearing on the synchronous vibrations and the sliding mode observer combining with the notch filter was used to eliminate adaptively the unbalance vibration of the rotor and to ensure the method without distinguishing the displacement stiffness force and the current stiffness force, and also not need to design an algorithm to compensate the influences caused by a power amplifier. The simulation and experiments were performed. Simulation results demonstrate that this method reduces the synchronous bearing force significantly;Experiment results demonstrate that this method reduces the synchronous vibrations from 0.053g to 0.012g, reduced by 77% even if the passive magnetic bearings cannot be controlled. Moreover, the method is not only suitable for the active-passive hybrid magnetically suspended rotors but also for the all-active magnetically suspended rotors.