This paper presents a systematic research for understanding mechanical shearing effects on the fluid flow and the solute transport behavior of rough fractures through a numerical simulation approach. The aperture fields were modeled based on a real rock fracture geometry and the normal displacement obtained from the shear-flow test. The fluid flow through the rough fracture under shear was simulated using a finite element code that solves the Reynolds equation, and the transport behavior through the rough fracture under shear was simulated calculating the advection–dispersion equation. The results show that the fracture apertures increase as the shear displacement increases, with a few major flow channels detected through the fracture. The shear-induced flow channels increase both flow connectivity and transport connectivity, which accelerate the movement of solutes in a particular direction and lead to early breakthrough of the contaminants. Adsorption, acting as a retardation term, has a decisive influence on the transport process. These results can give a basic knowledge of the hydromechanical and solute transport progress through fracture, and will be helpful to safety assessment for high-level radioactive waste disposal facilities.