The seismic performance of the pile foundations of bridges is very important in earthquake and geotechnical engineering. At present, the seismic design of a pile foundation only considers structural measures to ensure its seismic performance, which can lead to overestimation or underestimation of the seismic performance. Therefore, this study investigates the seismic design of a bridge using a three-dimensional finite element model. Under different seismic waves, the seismic response of a pile foundation was calculated, considering the soil-pile structure interaction, and the results were compared and checked. The results show that:(1) The internal force response of the pile is related to the frequency spectrum characteristics of the input ground motion; (2) for the pile foundation in a site, the result of finite element analysis is similar to that of the m method; (3) when the depth of pile cap is zero, the internal force of the pile body is relatively large, so it is necessary to take corresponding measures to reinforce the soil around the pile cap.