According to the complex geological conditions of the upper reservoir of a pumped storage power station, there are two medium width faults extending from the inside to the outside of the reservoir and the weak weathering layer of the foundation rock mass in the auxiliary dam area is relatively thick. In addition, the designed anti seepage scheme is impracticable. To address these problems, we established a three dimensional finite element seepage analysis model based on the geological structure, topography and anti seepage curtain design of the reservoir. The permeability coefficients of the foundation rock mass in the reservoir area and the groundwater levels at the typical points of the reservoir were firstly determined through inversion, then the effect of different depths of the anti seepage curtain on the seepage field, seepage flow and seepage gradients of different parts of the reservoir were analyzed and quantified, and based on which the optimal scheme of the depth of the anti seepage curtain was obtained. The results show that the depth of the anti seepage curtain near the faults at the riverbed and the periphery of the reservoir should be increased by 10 m. The depth of the left and right dam abutments should be respectively reduced by 10 m according to 3 Lu standard. The depth at the periphery of the reservoir with no fault and auxiliary dam should be reduced by 10 m. The research results can serve as a reference for the depth optimization of anti seepage curtain of similar hydraulic engineering.