Abstract: Accurate wave velocity model is essential for site effect analysis, while there is large uncertainty in determining the actual wave velocity. The simplified homogeneous and layered model is usually adopted, or the wave velocity is assumed to vary linearly, quadraticly and exponentially according to the drilling data. However, the effect of different velocity models on seismic response of the alluvial valley is not clear. It is attempted to reveal the influence mechanism through quantitative analysis both in frequency and time domains using an accurate finite element-indirect boundary integral equation method. The numerical results show that for incident low-frequency waves (), different velocity models have little influence on the surface displacement amplitude. As the frequency increases, the influence becomes more and more significant. The difference between the linear model and homogeneous model is highlighted. It is found that the high-frequency resonance and the basin edge effect in the case of linear models seem more remarkable, which lead to the concentration of earthquake energy mainly in the near surface layer, the surface displacement amplitude in the valley is significantly enlarged, and the duration of earthquake ground motion increases obviously as well. In addition, the alluvial valley shape and the incident angle also have significant influence on the scattering characteristics of seismic waves, and the focusing area varies for different wave types. It is necessary to obtain wave velocity structure and boundary geometrical features of actual alluvial valley for the accurate simulation of earthquake ground motion.