In order to study the dynamic response characteristics of the spatial crossing tunnel under the action of motor vehicles, taking the intersection section of Wuwu Tunnel of Hangzhou-Wenzhou High-speed railway and Xizhenshan Tunnel of Yidong Expressway as the engineering background, a three-dimensional dynamic calculation model was established by using the numerical simulation method and the subroutine was used to simulate the movement of motor vehicles. The acceleration, displacement, and stress response characteristics of a driving highway tunnel, adjacent side highway tunnel, and upper high-speed railway tunnel under the action of motor vehicle load are obtained, and the variation rule of structural safety degree of each tunnel is obtained by calculating the safety factor of the monitoring section at every moment in the process of driving. The results show that the influence of motor vehicle load on the driving highway tunnel is obvious, the influence is mainly concentrated under the driving position, and the safety degree of the vault decreases most during driving. For the upper high-speed railway tunnel and adjacent highway tunnel, the influence of motor vehicle load in the driving tunnel is mild on the whole, and the influence degree is closely related to the proximity distance. The response of the adjacent highway tunnel is mainly concentrated on the adjacent side of the tunnel with traffic, and the safety degree of the inverted arch center decreases most when the right tunnel is driving. The response of the upper high-speed railway tunnel is mainly concentrated in the inverted arch, and the safety of the left arch foot decreases most when the tunnel below is driving. The research results can provide a basis for daily operation monitoring of space cross tunnels, urban subways and other underground engineering and provide a reference for design optimization of similar spatial cross tunnel engineering.