Finite difference method (FDM) based on boundary-fitted coordinate (BFC) transformation is presented in this paper. The curvilinear grid system, with computational boundary being coincident with the physical boundary, is numerically obtained by solving the Poisson equation. Seepage analysis can then be done by FDM in a uniform transformed orthogonal coordinate system. The method was applied to analyze the steady seepage in a foundation pit, a lock foundation, and an embankment dam with a free surface. It shows that BFC transformation method can make it easy to fit and update the changeable free surface as well as to closely simulate the physical domain with complex geometrical boundaries.