Studying the evolution law of fracture surface roughness of Beishan granite under different loading rates is of great significance for evaluating the stability and sealing of the surrounding rock in Beishan underground laboratory. In order to obtain a three-dimensional roughness index with clear geometric and physical significance that can characterize the anisotropy of rock fracture surfaces, a new method for characterizing the roughness of rock fracture surfaces based on the principle of element projection, called the element projection method, is proposed. Taking Beishan granite as the research object, Brazilian disc splitting tests were conducted under five distinct loading rates. Three-dimensional laser scanning technology was employed to acquire point cloud data of the fracture surfaces of the specimens. A novel method was utilized to calculate the roughness of the fracture surfaces. Furthermore, by integrating mesoscopic morphology images, the correlation between the loading rate and the fracture surface roughness was systematically investigated. The results indicate that the loading rate has a significant effect on the fracture toughness and fracture surface roughness of Beishan granite. At low-to-medium loading rates, cracks preferentially propagate along grain boundaries (intergranular fracture), resulting in enhanced surface roughness. Conversely, at high loading rates, rapid release of accumulated energy at the crack tip promotes transgranular crack propagation, yielding relatively smoother fracture surfaces. Moreover, the fracture surface roughness exhibits pronounced anisotropy, characterized by lower values parallel to the crack propagation direction and higher values perpendicular to it. Finally, comparative analysis against traditional characterization methods (the Rs and Grasselli methods) confirms that the proposed micro-element projection method offers robust reliability and applicability for quantifying rock fracture surface roughness.