In order to find out the effect of site structure and distribution of cut-fill area on the seismic responses rules of Xigeda formation three-dimensional subgrade in Xichang, finite element method software is used to simulate the acceleration distribution on the surface of three-dimensional calculation models under seismic load. This paper discusses differences of subgrade seismic response from three aspects, including platform structure of the site, elevation mutation, and excavation and filling area. And there are four conclusions can be drawn. Firstly, the higher the elevation sites platform is，the greater the acceleration amplification factors are，especially in the changes of vertical acceleration amplification factors. Secondly, a sudden increase of elevation causes a sudden increase of vertical acceleration magnification factors, and acceleration amplification factors is getting smaller while extending to the platform inside. Thirdly, the acceleration amplification factors of filled area are greater than those of the excavation area. Fourthly, because terrain amplification of the seismic response is directional, three-dimensional calculation models should be used to numerical analysis. The results provide an important basis for the Xigeda subgrade base plan selection in Xichang and seismic design.