A three-dimensional finite element model of the geological and hydrogeological conditions of the Baihetan dam was developed to analyze the seepage control schemes. The model was used to model the seepage distribution characteristics of the dam foundation such as the soaking surface, the gross head, the hydraulic gradient and the seepage flow to analyze the seepage stability of weak intercalation. The analysis used steady seepage theory and accurate simulations of the drainage holes to simulate the seepage field for normal operation conditions. The results show that the dam foundation grouting curtain effectively prevents reservoir water leakage from upstream and effectively stops possible leakage channels. Drainage hole arrays significantly reduce the surrounding soaking surface area and drain leakage water from the dam foundation and abutments on both sides. There are large hydraulic gradients at the intersections of the bedding fault zone, fractural fault zone and grouting curtain and at the drainage holes, with small hydraulic gradients at other locations. The results show that the seepage control design scheme can effectively control the seepage and that the anti-seepage drainage design is reasonable.