3D finite element models of magnetic suspended control moment gyroscope structure are established by general finite element analysis software. Initial modal analysis scheme of the MS-CMG structure, in which the frame and gyro-chamber are analyzed separately, is described. A new modal analysis scheme that the MS-CMG is analyzed as a whole structure is presented. The connection between the gyro-chamber and frame is realized by defining a revolution pairs. The numerical predictions from two modal analysis schemes show obvious difference. The new scheme is more reliable since it simulates the real wok status of MS-CMG.