Barton's formula is one of the most widely used equations for estimating the shear strength of rock joints. The Joint Roughness Coefficient (JRC) in the equation is a crucial parameter of the shear strength because it controls the roughness of the profile. To explore the spatial characteristics of the roughness of a rock joint profile, a total of 86 actual rock joint profiles were collected from published researches and digitalized. The Profile Height Variation (PHV) for each profile group was analyzed statistically. The standard deviation of the PHV was found to depend strongly on the JRC value. This correlation of the standard deviation of the PHV with the JRC can be used easily to estimate the JRC of a given joint profile. Owing to the above statistical features of the PHV, any random profile with a given JRC can be generated for further analysis. Therefore, Direct Shear (DS) tests were simulated for two joint profiles (a randomly generated profile with JRC = 19.6 and Barton's standard profile with JRC 18–20) using the Discrete Element Method (DEM). The simulation results revealed that both of the joint profiles have similar joint shear strengths, indicating that the randomly generated JRC profile can function as a good artificial profile in an engineering simulation. Finally, DEM simulation also indicated that the shear strength of rock joints originates from the roughness of the joints, and shearing-off of the joints occurs at a normal stress larger than 4 MPa.