Abstract: Because underground structures are wholly embedded in the subsoil, their seismic response is mainly affected by the surrounding soil; therefore, the anti-earthquake analysis method used for structures on the ground is not applicable in this context. Regarding the intersection node of the double-deck main tunnel and the double-deck underground ramp at the Jiangnan open-excavation section of the Nanjing Weisan Road river-crossing tunnel project, this paper establishes a tunnel structure/foundation soil interaction model using the dynamic FEM method and conducts a dynamic elastoplastic time history analysis using the EL Centro seismic wave, Lomap seismic wave and Kebo seismic wave. The results show that: 1) when the foundation soil vibrates along direction y, the tunnel structure experiences the most unfavorable force conditions; 2) under the action of the three seismic waves, the peak values of the tunnel strain response are close to each other, with the maximum strain response induced by the EL Centro wave that causes partial concrete cracking; however, 3) the interstory drift ratios under frequent earthquakes and rare earthquakes are within the limits, represented by the fact that the steel bars do not yield, and the tunnel structure is still in the elastic deformation state. Based on this, the design scheme of the intersection node structure composed of a double-deck tunnel and a double-deck ramp can satisfy the specified requirements for aseismic performance.