To reveal the seismic response characteristics of pebble soil sites, a series of shaking table tests were conducted on a typical pebble soil site in Chengdu, Sichuan Province. The amplification coefficient of peak acceleration, the acceleration spectrum response, and the dynamic earth pressure response of the pebble soil site under different seismic waves and excitation intensities were studied, and the nonlinear effect of site seismic response and the relationship between dynamic shear stress and dynamic shear strain of soil were analyzed. Results showed that the surface layer of the pebble soil site has obvious amplification effect on the seismic wave, and the amplification coefficient of peak acceleration is between 1 and 1.4; the amplification effect of the lower layer is small, and the amplification coefficient is between 0.9 and 1.2. The pebble soil site has the function of low-frequency amplification and high-frequency filtering; the upper and lower limits of filtering frequency band gradually move to the low-frequency direction with the increase of excitation intensity. The soil is not damaged when the excitation intensity is small, and the dynamic earth pressure increases gradually during the earthquake. With the increase of excitation intensity, the dynamic earth pressure response decreases sharply and then increases gradually. Under the low-intensity seismic excitation (SN1), the middle soil first enters the nonlinear response stage, and the energy loss of seismic wave in the middle soil layer is the largest. When the excitation intensity is large (EL3), the soil has a large deformation, and the maximum dynamic shear strain of the soil is 1.7%. At this time, the amplification effect of pebble soil site on the seismic wave is obviously weakened.