Along with the exploitation of underground space approaching to the deep constantly, the high external water pressure is posing a big threat to the safety of lining structure. Drainage holes are often used to release the pressure in the engineering practice. An optimization analysis of the drainage hole layout based on the stress target of lining was carried out in this study. The effect of the drain hole diameter, spacing and entry depth in rock on the water pressure was studied by orthogonal numerical tests. The results showed that influencing factors can be ordered as entry depth, diameter and spacing, from a high influence to a low influence, and with the pore pressure increasing, the influence of different layout decreased. A week after lining installation, the influence of different layouts reached 0. 3 MPa. Therefore, to reduce the water pressure on lining and ensure the safety of the lining, it’s preferred to increase the entry depth. Through the range analysis, influences of factors on the lining security were obtained, and the optimal drainage holes arrangement scheme was determined as 2. 86 m in spacing, 0. 2 m in diameter and 0. 2 m in entry depth, which means a great significance for the drainage hole design of hydraulic tunnels.