Taking the 3D cross-engineering of Caomeigou No.1 Tunnel and Pandaoling Tunnel as an example, a shaking table test was carried out to study the effect of tunnel spatial position on seismic wave propagation characteristics and acceleration response of surrounding rock under earthquake seismic excitation. Based on the influence of the spatial position of the tunnel, the characteristic form of the surrounding rock between the cross section and non-cross section is divided, and the accelerometer layout scheme is designed. Based on statistical probability, the ratio of peak ground velocity to peak ground acceleration (PGA) was introduced to quantitatively characterize the characteristics of seismic wave propagation spectrum. Furthermore, the SPECTR calculation was used to obtain the regional difference in the seismic wave propagation potential damage potential displacement parameter (P d ). Under the influence of the spatial location of the 3D cross tunnel, the peak acceleration and motion duration of the seismic wave are mainly reflected in the variation of the section along the elevation direction. Low-frequency (≤20 Hz) seismic waves have a greater impact on the tunnel structure, and peak ground velocity/peak ground acceleration ratio has a positive correlation with the peak input energy of ground motion. The ultra-small net-spacing cross tunnel has a spatially distributed coupling deformation effect. The crown of the upper-span tunnel is highly sensitive to earthquakes and becomes a weak link in seismic design. These results help us provide a theoretical basis for the seismic design of the cross-tunnel.