Most existing models for fluid transportation within a single rock fracture tend to use a channel with two smooth parallel plates, whereas real fracture surfaces are usually rough and tortuous, which can produce a flow field significantly different from the smooth plate model. For fluid flow in a rough fracture, there are surface concave areas (SCA), where the fluid velocity is extremely low, contributing little to the fluid transportation. It is of great significance to quantitatively evaluate the impact of rough surfaces on fluid flow. Therefore, a numerical model for simulating Newtonian fluid through rough fractures is proposed, where synthetic surfaces are generated according to statistical analysis of natural rock fractures and can be quantified by several characteristic parameters. Equivalent hydraulic aperture (EHA) is proposed as one quantitative indicator for evaluating the impact of fracture roughness. Systematic studies were conducted for evaluating EHAs of rough fractures, which, combined with characteristic parameters of fractures, are used to build surrogate models for EHA prediction. It is found that the EHA is directly correlated with the fracture roughness, the mean mechanical aperture, and the standard deviation of aperture distribution. The developed surrogate models were verified to have a high accuracy for EHA prediction.