Precise control of a magnetically suspended double-gimbal control moment gyroscope (MSDGCMG) is of vital importance and challenge to the attitude positioning of spacecraft owing to its multivariable, nonlinear and strong coupled properties. This paper proposes a novel linearization and decoupling method based on differential geometry theory and combines it with the internal model controller (IMC) to guarantee the system robustness to the external disturbance and parameter uncertainty. Furthermore, by introducing the dynamic compensation for the inner-gimbal rate-servo system and the magnetically suspended rotor (MSR) system only, we can eliminate the influence of the unmodeled dynamics to the decoupling control accuracy as well as save costs and inhibit noises effectively. The simulation results verify the nice decoupling and robustness performance of the system using the proposed method. Precise control of a magnetically suspended double-gimbal control moment gyroscope (MSDGCMG) is of vital importance and challenge to the attitude positioning of spacecraft owing to its multivariable, nonlinear and strong coupled properties. This paper proposes a novel linearization and decoupling method based on differential geometry theory and combines it with the internal model controller (IMC) to guarantee the system robustness to the external disturbance and parameter uncertainty. Furthermore, by introducing the dynamic compensation for the inner-gimbal rate-servo system and the magnetically suspended rotor (MSR) system only, we can eliminate the influence of the unmodeled dynamics to the decoupling control accuracy as well as save costs and inhibit noises effectively. The simulation results verify the nice decoupling and robustness performance of the system using the proposed method.