In this study, we developed a method to control vibration of a superconducting magnetic bearing flywheel using a repulsive levitation system that combines permanent magnets and coils. Generally, in the repulsive type magnetic levitation system using only permanent magnets, the repulsive force in the levitation direction is strong, but it is unstable in other directions. Therefore, the pinning effect of high-temperature superconductors is used to increase the stability. However, the resonance in the radial direction was large, and countermeasures were required. Thus, we propose a method to suppress the amplitude by changing the radial stiffness. In this method, we changes the current applied to the coil inserted between the repulsion magnets. This makes it possible to change the radial stiffness. Vibration is controlled by changing the stiffness at resonance point. The above vibration control method was verified by experiments, and the usefulness of this proposal was clarified.