A seismic analysis method for cable-stayed bridges with pile foundation based on site-structure integrated model have been developed, incorporating the technique of finite element-infinite element boundary, surface to surface contact algorithm and time-domain explicit analysis. For a 202.5m+300m single tower cable-stayed bridge with group pile foundations, the longitudinal seismic response is analyzed based on the integrated model, focused on the effect of valley site and the characteristics of the ground motion under soil-structure interaction. The results indicate that the shape of the valley and the two-dimensional soil layer will affect short period components of the ground motion, and affect the seismic response of the structure accordingly. For the ground motion, the soil-structure interaction strengthens the components with period close to vibration period of the pile foundation, while has little effect on the components of larger period.