Aiming at the non-parametric and time-varying parametric uncertainty problems such as the external disturbances, smooth parameter variations and jump parameter changes existing in the robot satellite system with floating base, an adaptive variable structure trajectory tracking control method in Cartesian space is proposed. The dynamics equation in joint space of the robot satellite system with floating base is established based on the extended manipulator model, and the dynamics model of the system in Cartesian space is derived considering external disturbances to the manipulator and the base simultaneously. An adaptive variable structure controller is designed by adopting the composite adaptive control combined with variable structure control under the condition that the bounds of external disturbances and parameter variations are unknown, and the robustness analysis of the controller is performed. The simulation of a two-link planar robot satellite system with floating base adopting the control method presented is implemented. The simulation result shows that the end-effector of the robot satellite with floating base has a good capability of trajectory tracking in Cartesian space.