In order to study the evolution of fracture permeability under shear action, a Weierstrass random fractal function was used in Comsol to generate a single fracture, and the relative displacements of two fracture surfaces were adjusted to simulate shear action. Changes of fracture width under different shear displacements and the defined range of nonlinear effects under different flow rates were analyzed, the factors affecting fracture permeability in shear process were determined by using scatter plot and function curve fitting, and the quantitative relationship was given. The results show that the probability density distribution of the gap width meets the standard Gaussian distribution without shearing, but with the shearing process, the Gaussian distribution of the gap width is destroyed and only reflects parts of the characteristics of the standard Gaussian distribution. When the shear occurs, the permeability first has a decreasing process, and then fluctuate within a certain range. The smaller aperture is unfavorable to the water flow through near the contact area. When Re>96, the fluid begins to develop from linear to nonlinear. The influence of fracture aperture on fluid seepage characteristics during shear deformation of single fracture of rock is simulated, which provides some reference for analyzing the geothermal change caused by fracture deformation in geological bodies.