This paper numerically investigates the fluid flow behavior through single fractures with directional shear dislocations. Synthetic fractures are generated with directional shear dislocations, and the lattice Boltzmann method is used to simulate the fracture flow. With an ignorance of tortuosity effect, a notable overestimation of hydraulic conductivity is observed when the simplified local cubic law is used. During the closure process, the decreasing rate of conductivity is found to be highly related to the roughness of fractures. The conductivity of smoother fractures decreases faster than that of rougher fractures. By conducting simulations on fractures with a constant shear displacement, the effective conductivity is found to vary with the shear directions. The results show that the conductivity of rougher fractures is less sensitive to the shear directions than that of smoother fractures. As fracture surfaces come into contact, a sharp decrease in effective conductivity is observed and the decreasing trend flattens as the contact ratio continues to increase. A new model is proposed based on the bottleneck model to predict the conductivity of sheared fractures. By integrating the tortuosity and channeling effects into the original model, the proposed new model shows a better performance in predicting the conductivity, especially for fractures with rougher surfaces.