According to the creeping flow equation and Navier-Stokes equation, the paper set up single asperity rough fracture geometry physical model and simulated the seepage behavior of single asperity rough fracture and true formation fracture by using finite element method (FEM).It also comparatively analyzed the fluid flow characteristics and flow field distribution in the fracture. The paper defined two parameters of roughness that the coarse correlation R0 equals to 2A/bmin, inclined rough index R1 equals to 2A/λ.The analysis showed that the single fracture walls don't participate in fluid flow and viscous force has great influence; the rough fracture fluid forms a fan shaped distribution along the wall and may produce the phenomenon of “backflow”. The asperity height and density can be used to describe fracture surface roughness. The asperity height and fluid pressure difference showed a negative correlation, while the relation of asperity density and fluid pressure is positive. R0 and R1 are inversely proportional to the Reynolds number and flow rate. The critical value of R1 is 0.714.