A hybrid-trajectory based terminal sliding mode controller (TSMC) is addressed for a free-flying two-flexible-link space manipulator with an elastic base. In this system, there are unknown but bounded external disturbances and parameters. First, the Lagrange dynamic model of the manipulator was established by the momentum conservation. Second, a TSMC based on desired trajectory was proposed, by which the terminal trajectories were asymptotically tracked and periodic flexible vibrations were excited. Then based on virtual control force, hybrid trajectories were generated, in which the flexible variables, the joint angular displacement errors and the base’s attitude error were considered. Finally, a hybrid-trajectory TSMC was presented, by which the terminal trajectories were asymptotically tracked and the flexible vibrations were suppressed.