This study investigates the impact of multiscale surface roughness on shear behaviors of crystalline rock fractures. Employing wavelet decomposition, we analyze the multiscale features of 3D fracture surface roughness and characterize each roughness level using statistical parameters. Using a validated shear simulation model, we simulate the direct shear processes of mated fractures with a realistic fracture surface digitalized from the scanning of a granite sample under various normal stresses and decomposed surface roughness levels. The shear behaviors, including the peak and residual shear strengths, shear-induced normal displacement (shear dilation) and surface degradation of the decomposed fractures are analyzed. The results reveal a significant correlation between shear strengths and the multiple levels of surface roughness. For the first time, we demonstrate the crucial role of 3D multiscale surface roughness in determining fracture shear strengths and find that the surface unevenness notably affects the peak shear strength of unfilled and mated fractures, while the surface waviness controls the residual shear strength. The unevenness also can enhance the fracture dilation and surface degradation within a relatively short shear distance (∼1 mm). The findings offer valuable insights for a better understanding and estimation of the shear behaviors of unfilled and mated crystalline rock fractures in engineering practice.