To gain insights into the spatial distribution of non-penetrating cracks during the rock fracture process, a comprehensive uniaxial compression test is conducted on cubic gypsum specimens (100 mm × 100 mm × 100 mm) containing two non-penetrating cracks. The two pre-formed cracks are rectangular, with dimensions of 25 mm length, 2 mm width, and depths of 80 mm and 35 mm on adjacent sides of the specimen. The depth of the 80 mm crack can be adjusted from 0° to 150° in increments of 30°, while the other is fixed at a 45° angle. The results show that the spatial distribution of non-penetrating cracks can significantly influence the strength of the specimen. Initially, the strength of the specimen exhibits an upward trend and subsequently declines as the pre-crack inclination angle of the main rupture plane increases, ultimately reaching its pinnacle at 90°. The total percentage of tensile cracks in specimens with different inclinations are found to be 57%, 57%, 63%, 77%, 68%, and 61%, respectively. This change aligns seamlessly with the fluctuation in specimen strength as influenced by the angle of inclination. Non-penetrating cracks can also induce spalling on the specimen surface and give rise to anti-wing cracks, thereby exacerbating the spalling on the specimen surface. The inclinations of non-penetrating cracks can inevitably exert a certain influence on the propagation of neighboring non-penetrating cracks. Additionally, the macro-scale shear fracture of the specimen often occurs on the side of the non-penetrating crack that is deeper. The curved tensile fracture surface formed by the extension of the non-penetrating crack bears resemblance to the non-penetrating region in its ability to somewhat restrain the propagation of new cracks. Even under uniaxial compression, the spalling surface of the specimen containing spatial non-penetrating cracks frequently exhibits fracture characteristics belonging to I-III mode fracture, while its interior may display characteristics belonging to I-II-III mode fracture. These findings hold significant implications for comprehending and elucidating the genuine fracture process and three-dimensional fracture theory of rocks.