There are numerous hydropower projects built in western China, and the geological conditions of the alpine canyons in this area are complex, mostly consisting of deep overburden. Therefore, seepage safety and control have become one of the important issues that must be considered in the construction and operation of hydropower stations. This study takes a hydropower project as an example and establishes a three-dimensional finite element model of the reservoir area. Based on the saturated-unsaturated seepage theory, the three-dimensional finite element method is used to invert the natural groundwater seepage field in the reservoir area. Then, the finite element simulation analysis is carried out to obtain the seepage field distribution, seepage slope and leakage volume of the reservoir area under the impervious curtain scheme. The influence of the permeability coefficient and thickness of the anti-seepage curtain of the right bank ancient river channel is compared and analysed. The analysis results indicated that the impervious curtain scheme of the right bank ancient river channel is reasonable and effective, and the quality of curtain grouting should be paid attention to and ensured during the construction process.