In the control of space robots, flexible vibrations exist in the base, links and joints. When building a motion control scheme, the following three aspects should be considered: (1) the complexity in dynamic modeling; (2) the low accuracy of motion control and (3) the simultaneous suppression of multiple flexible vibrations. In this paper, we propose a motion vibration integrated saturation control scheme. First, the dynamic model of space robot with flexible-base, flexible-link and flexible-joint is established according to the assumed modes method and Lagrange equation. Second, singular perturbation theory is used to decompose the model into two subsystems: a slow subsystem containing the rigid motions of base and joints as well as the vibration of links, and a fast subsystem containing vibrations of base and joints. Third, an integrated sliding mode control with input restriction, output feedback and repetitive learning (ISMC-IOR) is designed, which can track the desired trajectories of base and joints with −3 orders of magnitude accuracy, while suppressing the multiple flexible vibrations of base, links and joints 50%–80% and 37% performance improvement over ISMC-IOR-NV were achieved. Finally, the algorithm is verified by simulations.