A fast algorithm is presented to invert the structure parameter of the horizontal multi-layer soil. The procedure is divided into two independent stages. First, Fredholm equation of the first kind with respect to the apparent resistivity is solved by the technology of decay spectrum to reduce computation time greatly. Second, the structure parameter of soil is determined by the generalized Newton-Kantorovich method, which is more robust and less noise sensitive because of using the generalized inverse algorithm to solve the nonlinear equation group. The numerical results show the validities and main features of the proposed approach.