Using Fourier transformation, the 3-D boundary value problem of electric field of point source on 2-D geoelectric section is converted into 2-D boundary value problem. Then we discussed the application of boundary element method for calculating apparent resistivity on layered medium which contains 2-D column body. The integral calculation of horizontal boundary is avoided because of the selection of basic solution. So, the number of all needed boundary cut joints are much less. Particularly, it need not calculate the partial derivative any more, unknown quantities are decreased very much, so that it calculates 2-D boundary value problem conveniently. And using Fourier inverse transformation, we can obtain electric potential in 3-D space. The mathod proposed in this paper requires less memory, less ariginal data needed for computer input, and has higher calculating accuracy.