The material property of soil significantly differs from that of pile, inducing the relative sliding or separation between soil and concrete pile during earthquake. The strong nonlinear contact behavior can directly affect the stress states of pile and soil near the interface, thus affecting the seismic response of superstructure. The real pile-soil interface does have a certain thickness due to the constraint relationship of concrete on pile, and the contact zone of related volumetric law does exist. A user-defined element (UEL) program based on modified Desai thin interface element is developed and then inputted into ABAQUS. In the modification process, Rayleigh damping is added into the interface element to simulate energy dissipation in the process of strong nonlinear contact behavior between soil and pile. Hyperbolic model is adopted in normal and tangential constitutive relation. Certain behavior pattern rules of modified Desai element on pile-soil interface are made to simulate the contact states such as bonding, sliding, separation and reclosing. A fine 3D pile-soil-structure model is developed to improve the effect of the modified Desai’s interface element on the dynamic response of superstructure. The result provides an instructive guideline for engineering design in time-history analysis.