Understanding of solute mixing behavior at 3D rough-walled fracture intersections is significant to accurately predict solute transport processes in complex fracture networks. The mixing in intersecting fractures is influenced by the complex fracture geometry, shear processes, and hydrodynamic conditions. In this study, a series of numerical experiments are conducted to investigate fluid flow and solute transport in crossed fractures subject to shear displacement. A 3D rough-walled fracture intersection is constructed using digitalized granite surfaces. Shear displacement parallel to the fracture intersection is conducted to establish a series of fracture intersection models subject to different shear displacements. The flow field is simulated by solving the Navier-Stokes equations and the solute transport is simulated by solving the advection diffusion equation. Mixing ratio is calculated to evaluate the solute flux redistributions at fracture intersections. Overlapping area is defined to quantitatively describe the intersection geometry and interpret the mixing behaviors. The results show that the streamlines are constant when Reynolds number is low and the concentration distribution varies with Peclet number increases from 0.1 to 100. Mixing ratio in 3D rough-walled models is of different ranges compared with 2D models. Shear displacement can change the channeling through the fracture intersections and enhance the mixing effect. The overlapping area at fracture intersections can be used to quantify the solute mixing ratio. An empirical relationship between the overlapping area ratio and the mixing ratio is proposed. The findings in this study offer valuable insight to understand the redistribution of solute transport process in sheared fracture intersections at local scale.