In the construction of the tunnel passing through the existing structure at an ultra-close distance, the existing structure will produce obvious deformation. It is very important to understand the deformation characteristics of the existing upper structure at different positions, especially to ensure the safety of the upper structure and improve the effectiveness of tunnel construction. In this study, the double-line tunnels of Qingdao Metro Line 4 passing under the Cuobuling station were taken as the engineering background, and a detailed 3D numerical model was established. This study comprehensively considered the on-site construction process, including grouting hardening, stress release of the excavated rock mass, grouting pressure and so on. The influence of tunnel excavation on the ground settlement was compared with or without a station structure, and the result was fitted with an empirical formula. Finally, the deformation of the station structure due to the excavation of the double-line tunnels was analyzed. The results of the analysis were as follows: (1) In the presence of the station structure, the excavation of the tunnels had a significant impact on the surface settlement. (2) The settlement of the sidewall caused by the excavation of the left-line tunnel was greater than that of the right-line tunnel, and the settlement at the junction of the sidewall and the bottom plate was smaller than that at other positions of the sidewall. (3) Compared with the roof and middle slabs, the floor of the station was more susceptible to the influence of tunnel excavation. Overall, the research could provide guidance and reference for similar double-line tunnels through existing stations.