The fractured rock masses are considered as non homogeneous and anisotropic permeable media. The optimal fitting for calculated and measured water level and seepage discharge of measuring points is made. The reverse problem to identify the coefficient tensors of permeability of the rock masses is transformed into an equivalent mathematical minimizing problem. To improve the convergence of iterative calculation, an effective term for penalty is added to the expression of the minimum optimization function. Hereby, the solution to three dimensional complicated reverse problems can directly be obtained on computer. Finally, the solution of a complicated practical example is presented in detail.