The southwestern region of China has deep river valleys and complex geological conditions. The locations of underground powerhouses are often close to the reservoir area. When the reservoir is possessed with water, the seepage flow will affect the safet and stable operation of the station. To reduce leakage to the powerhouse area and strengthen the seepage stability, a complex seepage control system which includes anti-seepage curtains, drainage hole arrays, and drainage galleries is adopted. Subsequently, numerical modelling is used to analyze the overall 3D seepage field of Yagen II underground powerhouse area. Numerical results including the water head, pore pressure and leakage amount are obtained, which demonstrate that the seepage control effect in the powerhouse area is significant, and the overall design scheme of the anti-seepage and drainage system is reasonable and effective.