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Objective The co-structure system of subway station (hereinafter referred to as 'co-structure system') realizes the connection and conversion between the box structure and the box frame structure through thick plates. Due to the unique structural form of the co-structural system, its seismic response law is currently unclear, further study on the characteristics of its seismic response is needed. Method Taking the co-structure system of a comprehensive utility tunnel and subway station as an example, the finite element simulation model of soil-co-structure system interaction is established. Considering one-way and two-way seismic waves (both horizontal and vertical) as inputs, three working conditions are selected. The acceleration response characteristics, displacement response characteristics, compressive and tensile damage situations, and the evolution process of the co-structure system under seismic action are analyzed. Taking the left column end of the co-structure system as an example, the internal force response characteristics of some structural parts are discussed. Result & Conclusion The vertical acceleration of the co-structure system is greatly affected by the bidirectional coupling ground motion. The maximum increase in acceleration at the joint between the side wall and the negative first floor slab reaches 158 % (compared with the vertical ground motion). Vertical ground motion may increase the relative horizontal and relative vertical displacements in the roof and floor of the co-structure system, and the internal force response of the column as well. Locations of the co-structure system such as the column ends, the lower part of the side wall, both ends of the bottom plate, the connection of the components, and the axillary angle are vulnerable to seismic damage, and should be strengthened accordingly.