In the process of calculating the analytical formula of the critical stable section area of the surge tank, the influence of the time constant of the flow inertia in the pressure pipe is ignored by all the formulas, including Thoma’s formula and the E/N correction formula. In this paper, a fifth-order analytical model of a hydraulic turbine generator set with a surge tank is established after considering the inertia of the flow in the pressure pipe. Then, the relationship between the flow inertia in the pressure pipe and the critical stable section area of the surge tank is systematically analyzed by using this fifth-order analytical model. Finally, combined with a typical hydropower station, the influence of flow inertia of the pressure pipe on the stable section of the surge tank caused by the changes of head, flow and the length of the pressure channel is analyzed.