The true triaxial stress are typical stress state in the deep underground. 3D surface flaws, one of the most common type of flaws, extensively existed in the rocks. Therefore, the study on evolution of the 3D surface flaw under true triaxial stress is crucial to determine the fracture behaviors of the rock in some deep underground spaces. Gypsum, as a rock-like material, has been extensively used in studies of crack initiation and propagation. In this study, we prefabricate a pair of 3D surface flaws at 45° in the cubic gypsum specimen and investigates the effect of the intermediate principal stress on initiation and peak stresses (characteristic stress thresholds) of flaws and crack propagation patterns of 3D surface flaws parallel to the intermediate principal stress. The true triaxial apparatus and acoustic emission (AE) technique were used to test and monitor the mechanical behaviors of the samples. The internal crack propagation pattern was observed by X-ray CT scan. The results demonstrate that the intermediate principal stress strongly affects crack patterns but has a limited influence on characteristic stress thresholds. Both the intermediate and minimum principal stresses affect the difference in the crack peak and initiation stress, which elucidates how the true triaxial stress affects the fracture behavior of the specimen. Additionally, the intermediate principal stress effect on characteristic stresses is closely related to the magnitude of minimum principal stress. When the magnitude of minimum principal stress is small, with the rising intermediate principal stress, the characteristic stresses increase slowly. When the magnitude of minimum principal stress is large, the intermediate principal stress almost has no effect on characteristic stresses. The surface wing cracks and anti-wing cracks initiate from the flaw when the magnitude of intermediate principal stress is relatively small. With the intermediate principal stress increasing, the surface crack propagation pattern is shift from tensile crack to shear crack. Through the CT image reconstruction technique, the propagation patterns of the inner tips of single 3D surface flaw were illustrated in this paper. It is observed that the large intermediate principal stress can restrict the crack wrapping and even make the internal flaw propagation patterns same with that on the specimen surface, providing insights into the validity of simplifying 3D flaws as 2D flaws for analyzing and computing crack propagation.