The transient analysis program (TAP) model is used to simulate the inflow process of Qianhai-Nanshan Drainage Deep Tunnel in Shenzhen. Through the simulation of design standards, exceeding standard and accident conditions, the risk of system surge generation is analyzed, and the relevant measures to control the surge are proposed. The study shows that in the 50 a and 100 a design rainfall scenarios, the highest total head line of the system is below the ground level. And the large-diameter shaft structure and additional ventilation shafts used in the system can effectively control the impact of surges.