Abstract: Based on the time domain implicit dynamic finite element method with viscous-elastic artificial boundary, the numerical simulation of seismic response of three-dimensional valley topography under vertical incidence of ground motion is realized. The influence of valley topography on ground motion, i.e. the difference of peak value and particle motion trajectory, is analyzed firstly, and then the frequency domain characteristics of ground motion such as coherence and phase difference are analyzed. The results show that the valley topography has a significant impact on the ground motion intensity, which is related to the characteristics of the valley and the location of site points. The valley topography can produce obvious ground motion conversion, and the bigger the slope is, the more obvious the ground motion conversion is. The effect of valley topography will weaken the coherence of ground motion. The ground motion on both banks of the valley has good coherence with each other. With the descent of slope, thecoherence is worse. The effect of valley topography leads to the phase difference of ground motion, and its magnitude is related to the location of site points. There is almost no phase difference between the ground motions on both banks of the valley, but the phase differences on slope and bottom of the valley are both large.