Building deep shafts in water-rich granite formations with large fissures has difficulties, such as high-water pressure and high construction risks, and is prone to water inrush and shaft flooding. This paper relies on the No. 1 vertical auxiliary shaft project of Gaoligongshan tunnel and obtains the uneven distribution of water pressure on the outside of the lining in the horizontal direction through on-site monitoring data. In order to explain this phenomenon, based on the statistical parameters of actual fractures in the field and the Monte Carlo method, the DFN built in FLAC3D6.0 is used to generate a discrete fracture network, and a dual medium model, considering the distribution of large fractures, is established. The reason for the uneven distribution of water pressure is obtained through research: the large fissures in the surrounding rock make the hydraulic conductivity of each part of the stone body formed after grouting of the surrounding rock different. This results in different osmotic pressures from the hydrostatic pressure outside the grouting ring to the outside of the lining through the grouting ring. Based on the distribution characteristics of water pressure outside the lining, the safety of the lining under non-uniform pressure is studied. The lining safety factor is defined as the ratio of the lining’s normal service limit state load to the actual load. The normal service limit state load is the load when the RFPA software is used to establish a load-structure model to simulate the load when the lining has obvious cracks under the action of external load; the actual load is the monitoring load. The new method and mine design code method are used to evaluate the lining safety and make a comparative analysis. The results show that the new method can effectively calculate the lining safety factor and has a larger safety reserve.