Abstract: During the CO2 injection and geological storage process, the integrity of the cap rock significantly influences the long-term safety of CO2 storage. Natural fractures within the cap rock serve as potential pathways for CO2 migration, thereby increasing the risk of CO2 leakage. In this study, we determined the types, developmental characteristics, permeability changes, and CO2-H2O-Rock reactions of natural fractures in the mudstone cap rocks of the Sanduo Formation (E3s) and Dainan Formation (E2d) in the Gaoyou Sag of the Subei Basin using core observations, thin-section analysis, rock mechanics experiments, and paleomagnetic directional analysis. We identified four tectonic fracture sets (NNW, NWW, EW, and NE); high-angle shear fractures, ranging from 60° to 90° (average 82°) and typically measuring 4‒12 cm (average 7.5 cm), dominate the assemblage, while slip fractures, ranging from 32° to 50° (average 36°) and measuring 3‒6 cm (average 3.9 cm), are also present. At the microscale, shear fractures average 160 μm, and bedding fractures average 82 μm. Notably, 85.78% of shear fractures are unfilled, with calcite filling observed in 14.22%, while other fracture types show no filling. Permeability tests on samples without fractures reveal that permeability declines rapidly below 9 MPa, especially in shallower samples, followed by a slower reduction between 9 and 13 MPa, and ultimately stabilizes at approximately 0.00003 mD. In contrast, samples with fractures exhibit permeability that is 3–4 orders of magnitude higher; their fracture permeability decays according to a power law with pressure yet remains above 10 mD even at 46 MPa. Fractures with larger dip angles and those aligned with the maximum principal stress demonstrate the highest permeability. While silicate-filled fractures exhibit negligible changes in permeability, carbonate-filled fractures experience a temporary enhancement due to dissolution; however, subsequent permeability remains controlled by factors such as effective stress and fracture orientation.