Abstract: A global model of equivalent modeling and a submodel of accurate modeling based on “abandoned hole algorithm” for densely deployed drainage holes are established respectively to simulate the complicated seepage control measures and geological conditions for the underground hydropower cavern area at the left bank of Jinchuan Hydropower Station. The long-term seepage control effects of the surrounding rocks of the underground powerhouse and the sensitivity analysis of seepage control measures for the project design are performed by using the stationary seepage analysis method and combining the variational inequality formulation of Signorini’s type with an adaptive penalty Heaviside function. The method of determining the hydraulic conductivity tensor is modified so that it can accurately overcome the disadvantage of ignoring the permeability characteristics of the fractured rock mass. The principal values and directions of the hydraulic conductivity tensor are first determined by the statistical method based on the measurements of the spatial spreading of fractures, and are then modified using the estimates of isotropic hydraulic conductivity that are calculated according to the water permeability rate from a field water-pressure test, and finally are verified using the inversion analysis. The results show that the integrated seepage-proof drainage system will control the water flow from the reservoir and mountain area efficiently; the cavern walls of generator floor and transformer room will be above the ground water surface under the operating conditions; the floor of the machine hall and the surge chamber are both under pressure slightly. The seepage distribution is not sensitive to the permeability of grouting curtains, auxiliary drainage hole arrays and spacing of drainage holes, which however can reduce the flux from drainage holes obviously. It is suggested that the quality for grouting curtain should be guaranteed and the auxiliary drainage hole arrays should be arranged. A spacing of 3 m can be taken for the drainage holes below the middle drainage tunnels and a larger spacing (e.g., 4.5 m) is suggested for those holes above the middle drainage tunnels.