Seepage control is one of the most critical technical problems in earth-rock dam construction, and seepage analysis is the main way to evaluate seepage control effect and optimize seepage control design. In view of the complex geological conditions and seepage control measures in the engineering area of Heihe Jinpen Reservoir, a three-dimensional seepage calculation model including the main (auxiliary) dam, dam foundation, reservoir basin and thin hill beam on the left bank was established. In order to ensure the stability and convergence of numerical calculation, the Signorini variational inequality method was used to simulate the long-term stable seepage in the dam area of Heihe Jinpen Reservoir. Based on the comparison and analysis between the measured results and the numerical results, the validity and correctness of Signorini variational inequality method in seepage analysis of earth-rock dam junction were demonstrated. Based on the numerical results, the seepage control effect and seepage stability of the dam area were deeply analyzed, and the sensitivity of seepage control effect on the permeability parameters of clay core wall, curtain and rock material was studied. The results indicate that the seepage discharge and the maximum hydraulic gradient of the key parts in the dam area of Heihe Jinpen Reservoir are all within the safe and stable range, and the seepage control measures are effective. The seepage control effect in the dam area is sensitive to the change of seepage control curtain and the permeability coefficient of mountain material, the tolal head and the hydraulic gradient of the key parts in the dam body increase with the increase of permeability coefficient of clay core wall. This research can be used for reference in the overall seepage analysis and seepage control optimization design of earth-rock dam area.