Based on the theory of discontinuous dynamical systems, this paper investigates the effect of the motion state of interface on the damping characteristics of SSI system through the phase plane analysis method. The necessary and sufficient conditions for the coordinated motion state of interface between soil and structure are obtained. The relationship between the motion state of interface and the damping system is investigated via the shaking table test. It is verified that the coordinated motion state of interface is the decisive factor for the identification of damping system. The phase trajectories of the interface and the transfer functions of the system after the different magnitudes of vibration are further given. The test results show that the motion coordination mechanism is developed between soil and structure. The coordination mechanism enables soil and structure to have a unified and collaborative motion state after a small magnitude of the vibration. The SSI system can be viewed as an approximately classical damping system under a certain dynamic excitation.