During shale gas production, the enhancement of stimulated reservoir volume is contingent upon the establishment of a three-dimensional (3D) complex fracture network. Supercritical carbon dioxide (SC-CO2) holds great promise as an emerging fracturing fluid, owing to its unique advantages in reducing breakdown pressure, forming high-roughness fractures, and inducing multiple fractures. However, the influence of geo-stress conditions on the 3D fracture characteristics and propagation behavior of shale using SC-CO2 fracturing remains poorly understood and merits further investigation. In this study, laboratory-scale true triaxial fracturing tests were conducted on Longmaxi Formation shale, with variables including fluid type, horizontal stress difference, and stress regime. Deep learning methods offer significant advantages in accurately identifying minute fractures induced by SC-CO2 fracturing, and thus the U-Net deep learning model and computed tomography (CT) technology were combined in this study to conduct 3D reconstruction and digital quantitative analysis of fractures. Additionally, acoustic emission (AE) signals of fractures during the shale fracturing process were collected and analyzed. The results indicated that: (1) The ability of SC-CO2 to activate bedding planes and the phase transition effect of CO2 were the two core mechanisms responsible for the generation of such rough and complex fractures during SC-CO2 fracturing. (2) A large horizontal stress difference coefficient would reduce the roughness and complexity of fractures induced by SC-CO2 fracturing. As the horizontal stress difference increased, the fracture propagation behavior of shale in SC-CO2 fracturing experiments gradually shifted from being dominated by bedding planes to being dominated by geo-stress. (3) The stress regimes (normal faulting or strike-slip faulting) exerted minimal influence on the complexity of the fracture network induced by SC-CO2 fracturing because of the small magnitude difference between the maximum and intermediate principal stresses. The fracture propagation behavior of shale under the above two stress regimes remained significantly governed by the bedding plane. (4) The fracture propagation patterns when a fracture induced by SC-CO2 fracturing approached a shale bedding plane were summarized as follows: activating, deflecting, penetrating, or composite. These findings provided a reference for the optimized design of SC-CO2 fracturing schemes for shale reservoirs under different geo-stress conditions.