The prediction of the free-surface seepage flow behavior in fractured rock mass is of significance in geotechnical engineering. There are two major issues in solving the seepage flow in complicated fractured rock mass based on the fractured porous medium (FPM) flow model, in which groundwater is assumed to flow simultaneously in both rock matrix and embedded fractures: One is the mesh generation of rock mass in the presence of the fracture network, especially when there exist a large number of stochastic fractures; the other is that a robust iteration algorithm is required since the free surface is unknown at the beginning of solution. Aiming at these two issues, this paper proposes a novel numerical method by coupling radial point interpolation method (RPIM) and finite element method (FEM), in which RPIM is utilized to model the rock matrix and FEM is utilized to model the fractures. On the basis of the variational inequality (VI) theory for free-surface seepage analysis, the computation formulations of the numerical method are derived and the corresponding computation program is developed. Three examples are solved with the present method. It is found that the VI theory can be extended to solve the free-surface seepage problem based on the FPM flow model. A crucial advantage of the present method is that the mesh generation can be greatly simplified. The present method has been verified to be a robust, efficient and reliable method for modeling the groundwater flow in complicated fractured rock mass.