A simplified analysis method based on three-dimensional finite element analysis is proposed for the dynamic response of pile foundations under the action of vertically propagating SV waves. This method considers the impact of upper structure inertia force and free field deformation on the internal force of the pile separately. The former is considered using the Equivalent Base Shear Method, while the latter is analyzed using a finite element response acceleration method for underground structures. This study selected three seismic waves and their average values as loads to calculate the dynamic response of pile raft foundations. Through trial calculations, the seismic effect reduction coefficient range (0.35–0.4) of the representative values of the horizontal seismic inertia force corresponding to the upper structure was obtained. The error between the peak shear stress of the pile top obtained by the quasi-static method and the time history analysis results was less than 10%. The research results indicate that the proposed simplified analysis method can accurately obtain the peak shear stress and its distribution pattern of the pile body under horizontal seismic action while significantly improving the analysis efficiency. This method has high accuracy and efficiency in conducting seismic design comparison and analysis of multiple foundation schemes.