Both mechanical and hydraulic behaviors of rock joints are closely dependent on joint aperture. Understanding how fracture wall roughness affects the fluid flow is important when modeling many subsurface problems. In this paper, a new evaluation method of joint hydraulic aperture using surface asperities height was developed, and the value of hydraulic aperture under different shear displacements was determined using the multi-scale wave decomposition method based on the wavelet theory and some statistical indices. For this purpose, a high-resolution laser scanning system was applied. The numerical simulations were based on the experimental data obtained by Sharifzadeh, Mitani, Esaki, and Urakawa (2004. Development of evaluation method of rock joint aperture distribution. EUROCK & 53 Geomechanics Colloquium) from a series of hydromechanical shear tests on natural granite rock joints. Using this method, the hydraulic aperture of joint surfaces has been developed for different shear steps to model the fluid flow of rock joints. The modeling procedure of mechanical aperture (or dilation) was precise and reliable. In addition, the proposed procedure appropriately estimated both hydraulic aperture and fluid flow rate. The conformity in the results of modeling and laboratory tests satisfactorily indicated the success of the proposed procedure.