Based on frequency domain method, the seismic responses of the superstructure-pile foundation-soil system are studied taking the dynamic soil-structure interaction into consideration. For analyzing the earthquake response of cylindrical pile foundation, earthquake response analysis of three-dimensional system of pile foundation-soil-superstructure simplify two-dimensional question. The dynamic responses of the interaction system under EI-Centro ground motion excitation are evaluated by using secondary development of the large general finite analysis software Abaqus. It is shown that pile foundation is more anti-seismic and that pile foundation flexibility can improve the structural basic cycle. Based on a comprehensive assessment theory, soil-superstructure interaction problem under Earthquake is analyzed by second-level evaluation of comprehensive evaluation. By applying comprehensive evaluation method fuzzy theory model of soil-superstructure interaction is built. It is show that fuzzy mathematics method is appropriate for this kind of soil-superstructure interaction problem.