The safety operation and the utilization of reservoir engineering benefits are significantly influenced by the existence of deep overburden foundation and the seepage dam leakage on both sides of the dam. Thus, it is necessary to take corresponding prevention measures to reduce the seepage discharge of dam foundation and dam abutment. The established three-dimensional finite element analysis of the case study can accurately reflect the main geological structure, dam body and dam foundation geometry. Considering the thickness of the cut-off wall at normal water level (0.6, 0.8, 1.0 and 1.2 m), extending the cross-strait abutment(50, 60, 70 and 80 m) and foundation ⑥-2 formation depth (3, 6, 9, 12 and 15 m), the seepage field characteristics and stability of the dam foundation and the abutment of the two sides are studied from the isoline of groundwater level, the seepage gradient and the seepage discharge. By increasing the thickness of the cut-off wall and extending the depth of the dam foundation and crossbar abutment, the distance between the groundwater level isoline of both sides of the dam and the cut-off wall decreases. Meanwhile, the head loss in the cut-off wall increases. The maximum percolation ratios of dams, dam foundations, and cutoff walls meet the requirements for seepage stability. Extending the depth of seepage walls deep into the abutments of both banks can effectively reduce the seepage ratio drop of abutments, and can also effectively control aquifer penetration and reduce the abutment surface of the abutment behind the wall. However, the changes on cut-off wall thicknesses cannot effectively control the seepage discharge of the dam foundation, and the depth of the dam foundation should be deepened to control the seepage discharge of the dam foundation. The finite element numerical model of three-dimensional seepage is established to optimize the seepage control scheme. This study can provide important basis for the evaluation of leakage and seepage stability of deep overburden foundation dams in China.