A robust task space tracking scheme is proposed for the free-flying space manipulator system. The dynamic equations of the system are derived via the law of momentum conservation, and then a linear state space representation is formulated by local linearization. A parametric approach is applied by using the eigenstructure assignment theory and the model reference method. A feedback stabilizing controller and a feedforward compensation controller are built based on the approach. Then an optimization procedure is followed after that to obtain the desired requirement and characteristics. Simulation results are presented to show the effectiveness of the proposed method.