The seismic response of a fabricated subway station is a complex structural connection problem that depends on the mechanical properties of the joints. In order to obtain the optimal joint distribution of a fabricated station structure under earthquake action, three finite element models of a single ring structure of fabricated subway stations assembled with seven, five, and four prefabricated components were proposed. Seismic wave characteristics, peak acceleration, and coupled horizontal and vertical seismic components were considered to study the seismic response of the fabricated subway station structure with different forms of the joint distribution. The dynamic time history method was used to analyze the seismic response in three aspects: structure plastic strain, interlayer relative deformation, and internal force. The damage indexes and residual strength indexes of the joints were offered based on the concrete damage index to evaluate the joints’ damage degree. The results showed that the joints of the vault or bottom plate had little influence on the seismic response of the fabricated station structure. The sidewall joints had the obvious seismic response and the most severe damage under horizontal ground motion or coupled ground motion, which were the weak joints of the fabricated station structure. The existence of vertical ground motion aggravated the damage degree of sidewall joints, making the damage occurrence time of sidewall joints earlier and the damage end time extended. On the premise of meeting the mechanical load and site requirements, an assembly scheme with fewer prefabricated components can be selected.