It　discusses　the　control　problem　of　space-based　flexible　manipulator　system　with　uncertain　parameters　to　track　desired　trajectory　in　inertial　space　when　the　attitude　of　base　is　controlled　and　its　location　is　uncontrolled.　Combining　the　linear　momentum　conversation　of　system,　the　dynamic　equations　and　the　Jacobian　relation　were　developed　by　using　the　Lagrange　approach　and　assumed　modes　methods.　A　singular　perturbation　model　of　the　space-based　flexible　manipulator　system　can　be　obtained　based　on　the　results　and　under　the　assumption　of　two-time　scale,　then　the　controller　can　be　designed　separately　to　track　desired　trajectory　and　to　suppress　vibration.　The　fast　subsystem　controller　damps　out　the　vibration　of　the　flexible　link　using　a　optimal　linear　quadratic　regulator(LQR)control　method.　For　the　slow　subsystem,　aiming　at　the　space-based　flexible　manipulator　system　with　uncertain　parameters,　a　composite　control　scheme　was　designed　on　the　base　of　a　computed　torque　controller　and　a　fuzzy　compensator　to　track　desired　trajectories　in　inertial　space.　The　numerical　simulation　shows　that　the　proposed　controller　is　feasible　and　effective.