Nonlinear flow in 3D rough-walled rock fractures is simulated by solving the Navier-Stokes equations. The emphasis is on the impact of shear-caused aperture changes (variable apertures and asperity contacts) and flow conditions (inertial term) upon nonlinear flow behavior. In order to compare shear effects, two 3D fracture models, with and without shear, were established with identical initial rough-walled surfaces topographies of a realistic rock sample. Five groups of simulations with different inflow boundary conditions of flowrates/Reynolds numbers (Re) were conducted to demonstrate shear-enhanced nonlinearity of flow fields and limitations of local cubic law (LCL) approach. The flow results clearly show channeling flow along the preferential paths, transverse flow around the contact spots, and eddy flows behind contact spots with increasing Re, which cannot be observed in 2D models. The effective transmissivity of the 3D fracture model was calculated from the modeling results of velocity and pressure fields. The results showed that the effective transmissivity is a function of local apertures with important uncertainties even when Re is small (i.e. Re = 0.4 in this study), thus the validity of the transmissivity evaluation using LCL approach for nonlinear flow in 3D rough-walled rock fractures is questionable. •Channeling and eddy flow behaviors in 3D rough-walled rock fractures enhanced by shear created asperity contacts.•Nonlinear relationship between flowrates and pressure gradients in the 3D fractures.•Nondeterministic relationship between effective transmissivity and local apertures.•Limitations of simplified 2D models in modeling nonlinear flow behaviors in rough-walled fractures.