In rock engineering, fluid flow and shear behavior have been considered as two significantly important issues in assessing the performance of many rock engineering fields, where understanding the fluid flow through single fractures and its coupling with shear is fundamental to better characterizing the flow and transport in fractured rocks. The roughness, matching degree and dilation incurred by shear increase the complexity of the geometrical characteristics of fracture, which may complicates the description of the fracture flow and lead to the deviation of the flow from linearity. In this study, the multiple relaxation time (MRT) model in the Lattice Boltzmann method (LBM) was adopted to simulate the fluid flow at moderate Reynolds (Re) numbers through a single granite fracture taken from the Beshan area. The nonlinear flow behaviors subjected to the shear displacement (ds) were numerically investigated. The numerical results indicate that the relationship between the flow rate and pressure gradient can be well represented by the Forchheimer’s law. The coefficients of viscous and inertial pressure drops experience an enlargement of one order of magnitude with the increasing shear displacement from 0 to 4 mm. It was found that the nonlinearity of fluid flow originates from the inertial effects induced by the roughness and the mismatching degree of fractures, besides the Reynolds number. The mechanisms of nonlinear flow, such as eddy flow, were well revealed and examined by calculating the effective advective apertures and the eddy flow apertures at different shear displacements, indicating that the effective hydraulic aperture of rock fracture is not constant but functions of the shear displacement and the velocity related to the Re numbers. This study provides an indispensable basis for understanding the nature of the nonlinear flow, the processes of mass and energy transport and their coupling with shear in real fractured rocks.