A model and simulate research about the effect of roughness in micro/nano-scale on waveguide inner surface was presented in this paper. The roughness in micro/nano-scale of the waveguide was simulated by an improved two-dimensional fractal function to investigate its power dissipation. The numerical integration method and the finite element method were employed as well as two approximate formulas were deduced to calculate the power dissipation of the local and global roughness respectively. As verification, a simulation experiment by a rectangle waveguide was involved. The comparison of two-dimensional fractal and two classical models (rectangle and one-dimensional fractal) indicated that the result of the two-dimensional fractal model was more close to the test data in high working frequency. The surface density had little influence on power dissipation, while the influence of fractal dimension was very strong. Following the increase of surface roughness, the power dissipation of the rough surface increased and the maximum of the increase was 1.8 times than that of the smooth surface.