The lithology of strata in mountainous cities is generally favorable, with relatively shallow soil cover. When constructing underground stations, a well-stressed arch structure is often preferred, but the overburden thickness often falls short of requirements, and deep rock excavation is costly. Consequently, a new prefabricated shallow-buried flat roof structure is proposed, and its mechanical characteristics are studied. The rail transit assembly station at Chongqing Logistics Park South Station serves as the engineering case. A fully reinforced concrete model was established, simulating soil layer effects using Python-based equivalent foundation springs. Comparative analyses of double T-beam, U-beam, and box-beam cross-sections were conducted, showing the double T-beam’s superiority in bending performance, deflection control, and stress characteristics. The force and deformation mechanism of the single-bay double T-beam assembled frame structure indicated that the medium plate and side walls experienced the largest deformation displacement, while the diagonal brace was the maximum stress point, prone to pressure damage. The reinforced concrete structure exhibited satisfactory load-bearing and operational performance. Finally, the design’s reasonableness was verified through a 1:1 structural assembly test, demonstrating a clear force transmission path, safe and controllable structural deformation, and meeting the bearing performance requirements for underground shallow-buried stations. This study provides a feasible solution for constructing underground stations in areas with shallow overburden, offering insights into optimizing structural design for similar projects.