The control moment gyro (CMG) must be installed on the vibration isolators for high-resolution observation satellites. However, the introduction of flexible support will inevitably cause resonance in the CMG control system, making it difficult to ensure the stability of the control system. In order to decrease the impact of flexible support on the stability of CMG gimbal control system, a resonance suppression method based on structural filter is designed in this paper. The designed structural filter is introduced in series into the closed loop CMG gimbal control system, which can attenuate the resonance in the gimbal control system caused by the flexible support and improve the stability of the CMG system. In the paper, the gimbal control system of CMG is described, and importantly, both simulation and experimental verification are conducted on the actual CMG control system. Simulation and experiment results verify the effectiveness of the proposed control method.