For Buguzi River Bridge on Wulumuqi-Kash Railway, a three dimensional soil-pile-structure nonlinear interaction system model was built. Long-period and normal seismic waves were selected for three dimensional seismic response parallel computation of soil-pile-structure nonlinear interaction system, and the interface effect of pile-soil and speedup ratio of parallel computation were discussed. The results have shown that the interface effect of pile-soil leads to considerable vertical in-coordination. When considering the interface effect of pile-soil, the horizontal acceleration response of piles is decreased little and the vertical acceleration response of piles is increased greatly when compared with uniform excitation. Meanwhile, the horizontal and vertical displacement responses of piles are increased. The horizontal acceleration responses of lateral pile caps are smaller than that of medial pile caps, and that of vertical acceleration responses are opposite. Parallel computing was also performed to raise computational efficiency.