The space docking process must be simulated on the ground to guarantee the success of the space docking task. By synthesizing a physical simulation and a numerical simulation, a hybrid simulator can simulate the complicated contact process of space docking. A hybrid simulator consists of a robot (i.e., lower platform), upper platform, docking mechanisms, contact force and torque measurement system, and numerical simulation system. To ensure the simulation accuracy, the robot is expected to have a high structure stiffness, high structure natural frequency, and high bandwidth frequency response. However, these performances are always limited in implementation. In this paper, how the structural dynamics of the robot affect the hybrid simulation accuracy is studied. Due to the structural dynamics of the robot, the divergence and convergence of the hybrid simulation are both possible. The stability conditions are given. A distortion compensation method for the structure dynamics of the robot is proposed. The stability analysis after the compensation is given. The software emulations and experiments are used to verify the analysis and the distortion compensation method. Experiments on real docking mechanisms are given to show the applications.