When the spacecraft with flexible appendages was undergoing large overall motions, such as orbit maneuvering and attitude adjusting, the driving mechanism of spacecraft might be disturbed by the rigid-flexible coupling effect caused by the vibrations of flexible appendages and the external excitation. First, the dynamic model of the spacecraft with flexible appendages was established. Then, the disturbance on the driving mechanism of spacecraft the caused by the vibrations of flexible appendages and the external excitation by the rigid-flexible coupling effect was researched. Finally, the results were explained by using the orbit maneuvering conditions and the inherent of flexible appendages.