The roughness of concrete lining is one of the essential parameters to evaluate the flow capacity of water conveyance structures such as concrete channels, tunnels, and aqueducts. In this paper, we develop an innovative method to calculate the roughness of a concave-shaped rough surface of concrete and to modify its effects on the seepage characteristics of a rough fracture. We also present the functional relationship between the surface roughness and pixel characteristic parameters of rough surfaces and investigate the effect of the roughness of a fracture surface on the flow capacity through a fracture. The results indicate that the unit discharge of a fracture is positively correlated with fracture aperture and roughness of the rough fracture surface. The relationship between the correction coefficient of the cubic law and relative roughness is represented by a quadratic polynomial. The calculated correction coefficients based on the modified formula match well with the experimental results. The mean absolute error (MAE), root mean square error (RMSE), and coefficient of determination (R 2) of the corrected calculated and test values are 3.35%, 0.0572, and 0.955, respectively. The proposed roughness characterization method and modified cubic law can thus effectively describe the seepage characteristics of concrete rough fracture.