The Desai thin-layer interface element is widely utilized in the simulation of interaction between piles and soil under seismic load. Conventional seismic analysis using the interface element cannot simulate the process of energy dissipation because tangential damping is disregarded. In this study, Rayleigh damping is added to the interface element to simulate energy dissipation in a strong nonlinear contact behavior. A user-defined element program based on a modified Desai interface element is developed. A hyperbolic model is adopted to simulate normal and tangential interaction behaviors. Certain behavior pattern rules of the modified Desai element, such as bonding, slipping, gapping, and reclosing, are defined. A three-dimensional pile-soil-structure model with a modified Desai interface element is established to investigate the effect of contact patterns on the inner force responses of a superstructure and pile foundation to an earthquake. Numerical results show that the contact patterns significantly influence the shear force, bending moment, and torque of the superstructure, while axial force is unaffected. With regard to the pile foundation, shear force and bending moment are also significantly influenced.