Discussing the development of the indirect boundary element method to the simulation of seismic dynamic interaction between river valleys and tunnels under Rayleigh wave incidence. On the basis of verifying the accuracy of the proposed method, the influences of tunnel buried depth and valley width-depth ratio on the surface displacement amplitude and circumferential stress of the lining tunnel under the action of the Rayleigh wave with different frequencies are quantitatively analyzed. The results show that: With the increase of tunnel depth, the displacement above the tunnel gradually decreases, and the amplification effect of surface displacement gradually weakens. The influence of the ratio of width to depth of the valley on the displacement amplitude in the valley and on the right side of the valley is more significant. Under shallow burial conditions, the circumferential stress amplitude coefficient of the tunnel near the river valley can reach more than 10.0, showing a significant dynamic stress amplification effect. Under η = 2.0 incidence, the amplitude-amplitude-amplitude-amplitude-is significantly affected by the valley width-to-depth ratio, but the amplitude-amplitude-effect is not obvious when the buried depth d = 3.0a. The seismic design of the tunnel along the river should focus on the amplitude effect of tunnel stress under shallow buried low frequency.