The rough structure in natural fractures will have impact on the fluid flow performance. It is difficult to understand its mechanism through direct research because of complex and disordered structure. In this context, a digital roughness crack model and introducing artificial roughness elements are constructed. And a crack simulation program based on the Lattice Boltzmann Method was written and verified to study the mechanism of the effect of crack roughness on seepage. The results show that: (1) Artificial elements with different shapes have different effects on fluid flow in the fracture, which are reflected in the local flow pattern. The rectangular element has the greatest obstruction effect on the fluid, and has the most developed vortex structure locally. The semicircular element and the triangular element have a decreasing effect on the fluid flow, and the degree of development of the local vortex is also reduced. (2) It is found that the interaction effect between height and distance disappears when the height is the same and the ratio of the distance and height between adjacent roughness elements is greater than 5 and two opposite vortices between adjacent rough elements merge into one. (3) The existence of roughness elements in rough fractures will have a strong viscous effect on the fluid. And with the change of the shape of the roughness element, the resistance strength of the viscous effect to the fluid is also different. The research results help to understand the seepage law of fluid flowing in rough fractures, and have certain reference significance for industrial applications such as oil production.