This study experimentally analyzed the influence of shear processes on nonlinear flow behavior through 3D rough-walled rock fractures. A high-precision apparatus was developed to perform stress-dependent fluid flow tests of fractured rocks. Then, water flow tests on rough-walled fractures with different mechanical displacements were conducted. At each shear level, the hydraulic pressure ranged from 0 to 0.6 MPa, and the normal load varied from 7 to 35 kN. The results show that (i) the relationship between the volumetric flow rate and hydraulic gradient of rough-walled fractures can be well fit using Forchheimer's law. Notably, both the linear and nonlinear coefficients in Forchheimer's law decrease during shearing; (ii) a sixth-order polynomial function is used to evaluate the transmissivity based on the Reynolds number of fractures during shearing. The transmissivity exhibits a decreasing trend as the Reynolds number increases and an increasing trend as the shear displacement increases; (iii) the critical hydraulic gradient, critical Reynolds number and equivalent hydraulic aperture of the rock fractures all increase as the shear displacement increases. When the shear displacement varies from 0 to 15 mm, the critical hydraulic gradient ranges from 0.3 to 2.2 for a normal load of 7 kN and increases to 1.8–8.6 for a normal load of 35 kN; and (iv) the Forchheimer law results are evaluated by plotting the normalized transmissivity of the fractures during shearing against the Reynolds number. An increase in the normal load shifts the fitted curves downward. Additionally, the Forchheimer coefficient β decreases with the shear displacement but increases with the applied normal load.