In this chapter, how the structural dynamics of the lower motion simulator affect the HIL simulation accuracy is studied. Due to the structural dynamics of the lower motion simulator, the divergence and convergence of the HIL simulation are both possible. The stability conditions are given. A distortion compensation method for the structural dynamics of the lower motion simulator 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.