Observer-based two-time scale robust control is proposed for free-flying flexible-joint space manipulators with unknown payload parameters and bounded disturbances. The dynamic equations of a free-flying space manipulator with two flexible revolute joints were derived by the momentum conservation law and the Lagrange equations. A flexibility compensator was introduced to make the equivalent joint stiffness large enough, which made traditional singular perturbation approach applicable. Then, a singular perturbation model was formulated and a reduced-order controller is proposed. This controller consisted of a slow sub-controller and a fast flexible-joint sub-controller. To the slow subsystem, a sliding observer based robust slow sub-controller was proposed. By optimal linear quadratic regulator method, the fast sub-controller was designed with the estimated velocity by linear observer. This fast sub-controller could stabilize the fast subsystem around the equilibrium trajectory created by the slow subsystem under the effect of the slow control. Finally the numerical simulations were carried out, which showed that elastic joint vibrations had been stabilized effectively and good tracking performances had been achieved.