The Xiaowan Hydropower Project is located in the middle and lower reaches of the Lancang River in Yunnan Province, China. The arch dam of this project, with a height of 294.5m, is by far the highest dam of its type that has been completed in the world. The great water potential makes it necessary to assess the seepage behavior in the dam-foundation system. Due to the complexity of geological conditions and seepage control system, the research is full of challenges. In this paper, the ﬁnite element method (FEM) is adopted to simulate the three-dimensional seepage field. The initial flow method and the boundary pre-adjustment method are combined to obtain the seepage free surface and overflow surface under complicated boundary conditions. The hydraulic potential contours, seepage gradient, drainage discharges, and so on, are all analysed and the results show that the seepage control system is reasonable and effective. Furthermore, the results of the seepage field can provide suitable seepage load in the stress-strain and stability analysis for the dam-foundation system of Xianwan. At present, the project is in good operation.