In view of the deep overburden foundation of the head hydraulic project of a diversion power station which results in high cost for the construction of the seepage control system according to the designed scheme, a three-dimensional finite element model for seepage analysis is established according to the geological structure, landform and seepage control system design of the dam site area of the project. Firstly, the distribution characteristics of seepage field in the reservoir area, the amount of seepage through various buildings and the seepage stability of the key parts are analyzed. The results show that the designed scheme meets the above requirements. Secondly, based on the designed scheme, the influence of changing the depth of impervious curtain and the length of curtain grouting holes on the left and right banks on the leakage is calculated and analyzed. Then the anti-seepage scheme is optimized according to the analysis results. The optimization results show that the depth of impervious curtain can be shortened to the middle line between the micro permeable zone and weak permeable zone, and the length of curtain grouting holes on the left and right banks can be shortened by about 10 m, so as to reduce the economic cost of seepage control system on the basis of effective control of the total leakage in the reservoir area.