The study of ground motion effects at river valley sites is an important guide to site selection and seismic design. In this paper, FLAC3D numerical simulation is used to explore the influencing factors of a river valley site. By selecting four influencing factors with different input ground motion spectrum characteristics, ground motion intensities, site slope angles and depth-to-width ratios, orthogonal test forms are designed to determine the calculation conditions, and numerical simulation analysis is conducted. The study obtains the ranking of influencing factors for the top section of the slope, slope section and valley bottom section at different locations of the river valley site. The main influencing factor is the spectral characteristics of the input ground motion; the main influencing factor of the slope section and the valley bottom section is also the spectral characteristics of the input ground motion; and the overall analysis of the amplification effect pattern of the trapezoidal valley site shows that the amplification effect of the valley bottom site is the smallest and that the amplification of the slope top site is the largest.