To effectively reject the gyroscopic effects and moving-gimbal effects of the double gimbal magnetically suspended control moment gyroscope (DGMSCMG) and to avoid high control effort, this paper proposes a novel control method based on modal decoupling strategy. Modal controller is employed to realize the modal separation of the translation and rotation modes of the magnetically suspended rotor (MSR). Then the dynamic coupling among the two rotation modes of the MSR system and the two rotational motions of the gimbal servo systems have been decoupled by using differential geometry theory. Dynamic compensation filters have been designed to improve the decoupling performance and the system stability without large control resource. Compared with the existing channel decoupling method, the presented one can not only realize the separate control of stiffness and damping of the MSR but also simplify the control system design significantly. The simulation results verify the effectiveness and superiority of the proposed method.