Three-dimensional seepage in double fractured media was modeled in this paper. The determination of hydraulic conductivity tensor of rock mass is a vital problem for the sea water intrusion or sea water encroachment and seepage of fissured medium. According to the geological and hydrogeological conditions for the 2nd-stage construction of the Three Gorges Project (TGP), the physical and mathematical models for the groundwater movement through the 3D double fractured media of rock mass during construction were established in this paper. Based on discontinuity-control inverse theory, some related parameters of double fractured media were inversed with flux being the known quantity and calibration of water table the objective function. Synchronously, the seepage field of the construction region was systematically analyzed and simulated, the results of which exhibit that the double fractured media model of fracture water can comprehensively and correctly describe the geological and hydrogeological conditions in the construction region.