The influence of surface roughness on fluid flow and solute transport through three-dimensional (3D) crossed rock fractures are investigated by numerical simulations. Three crossed fracture models with different degrees of surface roughness are established by two intersecting rough-walled fractures with four branches. The fracture surface morphological data are measured from three natural fractures in sandstone and granite rock samples. The fluid flow is simulated by solving the Navier-Stokes equations and solute transport is simulated by solving the advective-diffusion equation. By rotating one fracture plane while fixing the other, series of intersection models with different angles between the two crossed fractures are established to investigate the influence of the intersecting angle. Simulation results of the rough-walled fractures are compared with the smooth parallel-plate model, showing that the surface roughness significantly enhances channeling and mixing for fluid flow and solute transport at fracture intersections. The mechanism is that the complex geometry of the intersection for rough-walled models results in reallocation of fluid pathways at the intersection, which consequently affect the mixing behavior depending on the Peclet number. The intersecting angle affects the channeling and mixing behavior because it influences the geometrical structure of the fracture intersection. The correlation between the mixing ratio and the geometrical characteristics of intersections is quantified by a relative roughness parameter. The results reveal that the widely adopted smooth parallel-plate model may lead to significant uncertainty in predicting the solute transport in crossed fractures, especially at intersections with unmated fracture surfaces. The correlation between the mixing ratio and the roughness parameter developed in this study can be incorporated into discrete fracture network models to improve their performance in estimating solute transport in fractured rocks.