The formulas of three-dimensional (3D) electric field of radially polarized beam focusing through the interface of two dielectric media are deduced based on the vectorial Debye theory. The electric field in a defocus plan calculated by Debye theory is introduced into 3D finite difference time domain(FDTD) program as input source for the simulation of focusing process. The FDTD simulation results agree well with that calculated by Debye theory. Due to its facility of setting the structures for different media, the FDTD method is applied for simulating the problem of radially polarized beam focusing through half ball shaped nano-holes which can not be calculated by Debye theory. The focus shift and field intensity enhancement phenomena caused by the half ball shaped nano-holes are observed and analyzed.