The rapidly increasing demand for the consumption of natural gas has attracted the interests to store natural gas in aquifer reservoir. However, natural gas injected into the aquifer reservoir, which could cause ground surface deformation and mechanical integrity destruction of caprock. Taking the aquifer gas storage of S trap as the research object, according to the geological structure and hydrogeological information, a coupling large-scale hydromechanical model is established to evaluate the damage risk of the gas reservoir in S aquifer. The proposed methodology is based on the development of fluid-solid coupling and application of FEM. The different failure mechanisms of S aquifer gas storage caprock can be evaluated on the basis of the tensile failure criterion and Mohr-Coulomb shear failure criterion. To analyze the change of caprock in gas injection and production process more clearly, a reference model is defined as an ideal calculation condition to discuss the mechanical response, pore pressure variation, and surface deformation characteristics of the caprock during injection and production. On this basis, the second scheme of sensitivity analysis is defined. The pressure injection rate, reservoir parameters, in situ stress, and other factors are considered, respectively, and the influence of different input parameters on mechanical stability and surface deformation of caprock is analyzed. Finally, the mechanical stability is analyzed and combined the above two criteria to predict the upper limit injection pressure of S. Simulation results show that the permeability and in situ stress have a significant influence on ground surface deformation and mechanical integrity of caprock, but Young’s modulus and Poisson’s ratio can be ignored; the upper limit pressure coefficient of S is 1.908.