Based on the engineering practice of the first prefabricated subway station (Shuangfeng Station) in Changchun, China, the applicability of prefabricated subway station structures (PSSSs) in liquefiable sites in seismically defended areas is investigated. In this paper, the finite difference software FLAC3D 5.0 is used to carry out the seismic response analysis of the PSSS in liquefiable ground, and the calculation results of the PSSS are compared with those of the same type of cast-in-place subway station condition. The results show that the trend of foundation excess pore pressure ratio (EPPR) in the PSSS condition is similar to that of the cast-in-place condition. For different ground vibration inputs, there is not much difference between the PSSS and the cast-in-place structure on the pore pressure (PP) of the surrounding liquefiable soil. The acceleration response of the PSSS is slightly smaller than that of the cast-in-place structure, and it has a better ability to adapt to ground deformation. The deformation of the upper part of the PSSS is slightly larger than that of the lower part, which is an important part of its deformation control, and the middle part is the key part of its strength control due to the presence of the center plate, which results in a significant increase in stiffness and stress. The flexible connection of the PSSS is easier to adapt to a larger vertical deformation than rigid connection, and its ability to resist overturning is better. Under the premise of ensuring static waterproofing, the PSSS can be constructed in liquefiable sites in earthquake-proof areas.