In order to further explore the structural dynamic response and damage status of the upper tower subway station and promote the development of the TOD (transit-oriented development) model system oriented by public transportation, the seismic vulnerability analysis of the upper tower subway station structure in the TOD model was carried out. Taking an urban complex project in Beijing as the research background, a nonlinear analysis model of soil-structure interaction under different site types was established by considering the influence of site types, input ground motion characteristics and other factors. A seismic performance evaluation index range of the upper tower subway station structure in TOD mode was proposed and its seismic vulnerability curve was determined, and then the exceedance probability under different damage states was obtained. The results show that the corresponding seismic performance index ranges of the upper tower subway station structure under the five damage states of basically intact, slight damage, moderate damage, severe damage and collapse are [0, 0.136%], (0.136%, 0.324%], (0.324%, 0.664%], (0.664%, 1.122%] and (1.122%, +∞), respectively. The near-field pulse-type ground motion has a greater impact on the ground motion of the structure under the Class Ⅱ site, while the far-field long-period ground motion has a greater impact on the structure under the Class Ⅲ site. Compared with near-field pulse-type ground motion and ordinary ground motion, far-field long-period ground motion is more sensitive to site category. The ground motion characteristics and site types have a significant impact on the dynamic response of the upper tower subway station structure under the TOD mode. Compared with the site type Ⅱ, the ground motion characteristics of the site type Ⅲ have a more significant impact on the structure and the structure is more vulnerable to earthquake damage. The established seismic vulnerability curve and seismic damage probability table can effectively evaluate the seismic performance of the upper tower subway station in TOD mode. The research results can provide valuable reference for the seismic performance evaluation of similar underground structures.