In this paper, three typical bedrock long-period seismic waves and two commonly used waves were selected for three dimensional seismic responses parallel computation of a valley topography site under uniform excitation and traveling wave excitation. The equivalent-linear analysis method was used in simulation of soil’s non-linear properties. Computation results showed that horizontal acceleration response increase and vertical acceleration response decrease under long-period seismic wave excitation compared with those under commonly used waves excitation. When considering wave traveling effect, the horizontal acceleration response decrease and the vertical acceleration response increase. The conclusions are useful for relevant engineering projects. Parallel computation was also performed to raise computational efficiency.