Challenges related to seismic performance and seismic mitigation are more pronounced in the presence of weak interlayers compared to typical layered soil conditions. This study focuses on a double-layer double-span rectangular frame subway station structure. A coupled static–dynamic finite element analysis model of the soil-structure system is established by using the finite element software ABAQUS/CAE V 6.14. The research investigates the influence of factors such as interlayer thickness, location, and strength on the seismic response of subway station structures. Furthermore, in order to evaluate the effectiveness of FPB in mitigating seismic effects in the weak interlayer ground, two different schemes are proposed in this paper. One is the structure without FPB and the other is the structure with FPB on the top of the central column. The findings reveal that weak interlayers exert a significant influence on the seismic response of subway station structures, especially when these lower-strength weak interlayers are located within the central portion of the subway station structure and exhibit considerable thickness. The FPB on the top of the central column can reduce the overall lateral stiffness of the subway station structure. This, in turn, results in a slight increase in the deformation of sidewall and inter-story displacement angles, accompanied by a marginal exacerbation of sidewall damage. However, the implementation of FPB effectively reduces the deformation of the central column and substantially mitigates the extent of damage to the central column.