To study the dynamic response rules of pile foundations of mega-bridges over faults in strong seismic areas, a finite element model of the pile foundation-soil-fault interaction of the Haiwen Bridge is established. The 0.2-0.6 g peak acceleration of the 5010 seismic waves is input to study the effect of the seismic wave of different intensities and the distance changes between the fault and the pile foundation on the dynamic response of the pile body. The results show that the soil layer covering the bedrock amplifies the peak pile acceleration, and the amplifying effect decreases with increasing seismic wave intensity. However, bedrock has less of an effect on peak acceleration. The relative pile displacement shows the mechanical properties of elastic long piles. The pile foundation generates a large bending moment at the bedrock face and the upper soil layer interface, and a large shear force at the pile top and the soft-hard soil body interface. The relative displacement, bending, and shear bearing characteristics of the pile foundations on the upper and lower plates of the fault are significantly different. The deformation characteristics are affected by faults in a region ten times the pile diameter. Analysis of the dynamic p-y curves shows that the soil resistance on the pile side of the lower plate at the same depth is greater than that of the upper plate. Sensitivity of the dynamic response of pile foundations on either side of the fault to the effects of seismic intensity and distance between the pile foundation and the fault: distance l > seismic intensity q.