Abstract: Shazaoyuan granite masses are a substitute location for high-level radioactive waste disposal in China. The widely distributed stochastic discontinuities in the granite bodies in this area are crucial factors that control rock deformation and nuclide migration. The spatial distribution of stochastic discontinuities in the Shazaoyuan granite bodies was examined by considering the outcrop joints and borehole fractures within the range of 600 m×600 m×600 m. First, an analysis of the occurrences of stochastic discontinuities was performed, and the K-means algorithm based on particle swarm optimization was employed to cluster the occurrences. Stochastic discontinuities with dips >65 ° and strikes in the north-northeast (NNE), east-west (EW), and northwest (NW) directions were primarily developed in the rock mass. The dominant sets of borehole cracks were four, namely, 295.4°∠68.3°, 189.5°∠71.2°, 235.6°∠69.2°, and 66.0°∠33.0°, while the dominant sets of outcrop joints were four, namely, 320°∠79 °, 180°∠77°, 282°∠80°, and 231°∠67°, with both sets displaying similar characteristics. Second, planar analysis was performed on the outcrop joints. The Voronoi method was utilized to dissect the rock surface based on the outcrop location. The average trace length value and midpoint surface density value of the outcrop joints were employed to characterize the segmented polygonal rock mass. Based on the calculated values of complete outcrop joints, the average trace lengths in the northeast of the rock mass were about half that in the southwest, whereas the midpoint densities were the highest in the middle of the rock mass. Based on the calculated values of split outcrop joints by the dominant sets, the average trace lengths of the northeast (NE) and NNE oriented discontinuities were longer than those of the other dominant groups. The midpoint plane density values were higher. Finally, a depth analysis of the borehole cracks was performed. Based on the cluster analysis results of the occurrences of borehole cracks, the distribution maps of the strikes and dips of the different dominant sets in borehole cracks with depth were drawn. The borehole cracks demonstrated uneven depth distribution characteristics with an average linear density of 0.11 m^–1, reaching the maximum value of 0.60 m^–1 in the −150 m, −160 m depth, and the NNE cracks were densely developed in the −310 m, −370 m depth. This research results provide a reference for selecting better locations for storing high-level radioactive waste in this area.