The law of bonding and deformation of sprayapplied wagterproofing lining under seepage field is unclear, which affects the application and popularization of sprayapplied waterproofing lining structure. To address this problem, a highspeed cross tunnel is taken as the research object. First, the varied forms of waterproof layers for different waterproof lining structures are simulated using the builtin interface elements of FLAC3D finite difference software based on tested interface normal and circumferential parameters. Then, the surrounding rock seepage field and lining permeability performance are given attributes through the builtin seepage modes, and the mechanical properties and interface characteristics of different lining structures are compared and analyzed. Finally, the mechanical properties of sprayapplied waterproofing lining are obtained under different seepage fields. The results indicate the following. (1) The waterproof layer has a considerable impact on lining stress. Adopting an appropriate waterproof membrane structure can improve the collaborative stress capacity of the lining concrete; however, it causes an accumulation of water pressure behind the lining. This effect is more significant under longterm rock loading and high water pressure. (2) Under high waterpressure conditions, the structural stresses of the sprayapplied waterproofing lining differ from those of the traditional composite lining; in particular, the changes in internal force and safety factors should be examined. (3) The economy of the lining should be improved under the condition of the safety of tunnel operation. For the construction sections in which high water pressure is likely, adopting measures such as drainage design and lining structure optimization is recommended.