The 2-D finite-difference frequency-domain method (FDFD) combined with the surface impedance boundary condition (SIBC) was employed to analyze the propagation characteristics of hollow rectangular waveguides at Terahertz (THz) frequencies. The electromagnetic field components, in the interior of the waveguide, were discretized using central finite-difference schemes. Considering the hollow rectangular waveguide surrounded by a medium of finite conductivity, the electric and magnetic tangential field components on the metal surface were related by the SIBC. The surface impedance was calculated by the Drude dispersion model at THz frequencies, which was used to characterize the conductivity of the metal. By solving the Eigen equations, the propagation constants, including the attenuation constant and the phase constant, were obtained for a given frequency. The proposed method shows good applicability for full-wave analysis of THz waveguides with complex boundaries.