The mechanical properties of joints are important factors affecting the safety and stability of rock mass. The joint roughness coefficient (JRC) is a parameter for describing the roughness morphology of the joint surface, and its accurate quantification is very important to predict the shear strength. In the current statistical parameter methods for the estimation of joint roughness, the size of different protrusions on the joint surface was completely ignored, which did not correspond to the real failure mechanism of rock joint during the shear process. In this study, a new statistical parameter WPA was proposed for the estimation of JRC considering the shear direction and the contributions of different protrusions. First, the 10 standard roughness joint profiles were digitized based on image processing technology, and the obtained coordinate data were proved to be reliable by the calculation results of existing parameters. Secondly, the WPA value of 10 standard roughness joint profiles was calculated at a 0.5 mm sampling interval in two directions. The functional relationship between WPA and JRC indicated that they should be established in the same shear direction to maintain a high correlation. The JRC values of 10 standard roughness joint profiles in direction 2 were obtained based on the functional relationship established between WPA and JRC in direction 1, and the roughness of these 10 joint profiles was confirmed to be influenced by direction. Next, the effect of sampling interval on WPA was investigated. As the sampling interval increases, the WPA values gradually decreased and the correlation between them and JRC gradually declined. In practical application, a smaller sampling interval was recommended for more accurate prediction. Finally, the geometric coordinate data of 21 joint profiles given in the literature and 4 natural joint surfaces were obtained by graphics processing technology and 3D scanning technology, respectively. The JRC values of them were separately estimated by WPA in different directions. The results showed that the new statistical parameter WPA proposed in this paper can well describe the joint roughness considering the shear direction and the contribution of different protrusions.