In the seismic design of pile foundations, a p-y curve representing the nonlinear behavior of the ground considering the dynamic load of the earthquake is required. Recently, p-y curve analyses reflecting the soil-structure interaction have been conducted, but studies on multilayer structures have not been investigated extensively. In this study, the p-y curve characteristics were analyzed, considering the influence of the ground-structure interaction based on the mode shape of the structure (no structure, single-story structure, and three-story structure) through shake table tests. It was found that (1) the bending moment and pile displacement increased with input acceleration, and (2) the maximum soil resistance and pile displacement occurred at the natural frequencies of each structure were observed. In addition, the bending moment, soil resistance, and p-y curve slope were higher in the single-story structure than in the three-story structure. The findings indicate that the seismic design simulated for a single-story structure is conservative.