The seismic vulnerability of interaction system of saturated soft soil and subway station structures was explored in this paper. The coupled nonlinear numerical models of interaction system were established using the u–p formulation of Biot′s theory to describe the saturated two-phase media. A refined finite element model of interaction system was developed to study its nonlinear seismic responses and seismic hazard mechanism. In this study, the multi-yield elastoplastic constitutive model was adopted for the soil, while a fiber section elastoplastic constitutive model was used for the structure. The seismic response of the structure was calculated by inputting the artificial seismic wave obtained from the power spectrum-triangular series method. The maximum inter-story drift angle was taken as a structural performance parameter for the subway station structure. The structural demand cloud was obtained under random ground motion sequences. Based on the probabilistic seismic demand model analysis method, the seismic vulnerability curve of the subway station structure was plotted, and the seismic vulnerability curve was analyzed as per the vulnerability of performance parameters. With the increase of soil strength, the vulnerability index of subway station structure under different peak acceleration ground motion decreased correspondingly. Based on the above vulnerability theory and analysis methods, it can be found from the above vulnerability theory and analysis methods that the subway station structure with established buried depth in saturated soft soil site exhibits a certain degree of safety and reliability, and can meet the seismic fortification goal of "no damage in small earthquakes, repairable in medium earthquakes and no collapse in large earthquakes". The results of vulnerability analysis are in line with the actual seismic survey, and the vulnerability analysis method proposed in this paper can be applied to the vulnerability analysis of underground structures on saturated soft soil foundation.