In seepage flow simulation, the directions of principal permeation are not always coincided with the axises of global computational coordinates because of complex geologic structure of the natural porous medium. When the traditional method is applied, it can result in an illness discreted coefficient matrix and incorrect solution as a result of the fact that it is not a diagonal-dominance matrix. On the basis of anisotropic governing equation, a new method to divide the permeability tensor into two parts, diagonal elements and non-diagonal ones, then a differed correction method was employed to approach anisotropic model. The cross-partial derivative terms introduced by the anisotropic orientations were taken as source/sinks terms which can be easily handled by differed correction method. This method improves the diagonal dominance condition and raises the numerical accuracy and numerical stability.