To rationally and economically select a feasible lining structure for the shield section of the Jintang subsea tunnel of the Ningbo-Zhoushan railway, the characteristics of the subsea shield tunnel such as ultrahigh water pressure, ultralong distance, complex sea environment, and challenges in disaster prevention, evacuation, and rescue are summarized. A comprehensive comparison of single- and double-layer lining structures is conducted in terms of structural stress and deformation, specific subsea working conditions, longitudinal seismic response, and risk mitigation. This analysis establishes the necessity, feasibility, and economic advantages of the double-layer lining structure. In addition, the double-layer lining structure section is optimized to enhance the effective clearance area and subrail structure type, enabling the realization of a full-ring superimposed double-layer lining. The findings reveal the following: (1) Under static load conditions, the structural deformation of the double-layer lining scheme is relatively small, benefiting track smoothness, though comparable to the single-layer lining scheme. Space should be reserved for secondary lining, considering the complex construction environment of the sea section and long-term safety. (2) Under longitudinal earthquake conditions, the composite lining structure, consisting of the secondary lining and segment, demonstrates stronger connection performance, jointly bearing the load. This significantly reduces the peak deformation and stress of the segment, with a maximum decrease of 20.58% at the crown. Shock absorption measures address the vulnerability of the secondary lining to tensile damage. (3) Using the R=P×C grading risk assessment method, the risk reduction cost (RMB 342 million) is lower than the expected risk loss cost (RMB 347 million), indicating the superiority of the double-layer lining structure. (4) The effective above-rail net clearance area is optimized to 83.79 m², resulting in a reasonable change in the maximum stress on the train surface and transient pressure. The net clearance area is 4.3% less than the double-layer lining with a net clearance area of no less than 90 m² and a cross-sectional diameter of 14.6 m. (5) Based on disaster prevention, evacuation, and rescue requirements, as well as the aerodynamic effects of the cross-section, the subrail structure type is optimized. The circle range of the full-ring superimposed double-layer lining achieves 90.70%, with the cross-section diameter reduced by 2.1% compared to the full-ring 30 m cast-in-place secondary lining, which has a cross-section diameter of 14.3 m.