Permeability is a crucial parameter in the exploration and development of oil and gas reservoirs, particularly in unconventional ones, where fractures significantly influence storage capacity and fluid flow. This study investigates the fracture permeability of granite reservoirs in the South China Sea, introducing an enhanced evaluation model for planar fracture permeability based on Darcy’s law and Poiseuille’s law. The model incorporates factors such as fracture heterogeneity, tortuosity, angle, and aperture to improve permeability assessments. Building on a single-fracture model, this research integrates mass transfer equations and trigonometric functions to assess intersecting fractures’ permeability. Numerical simulations explore how tortuosity, angle, and aperture affect individual fracture permeability and the influence of relative positioning in intersecting fractures. The model makes key assumptions, including minimal consideration of horizontal stress and the assumption of unidirectional laminar flow in cross-fractures. Granite outcrop samples were systematically collected, followed by full-diameter core drilling. A range of planar models with varying fracture apertures were designed, and permeability measurements were conducted using the AU-TOSCAN-II multifunctional core scanner with a steady-state gas injection method. The results showed consistency between the improved model and experimental findings regarding the effects of fracture aperture and angle on permeability, confirming the model’s accuracy in reflecting the fractures’ influence on reservoir flow capacity. For intersecting fractures, a comparative analysis of core X-ray computed tomography (X-CT) scanning results and experimental outcomes highlighted discrepancies between actual permeability measurements and theoretical simulations based on tortuosity and aperture variations. Limitations exist, particularly for cross-fractures, where quantifying complexity is challenging, leading to potential discrepancies between simulation and experimental results. Further comparisons between core experiments and logging responses are necessary for model refinement. In response to the challenges associated with evaluating absolute permeability in fractured reservoirs, this study presents a novel theoretical assessment model that considers both single and intersecting fractures. The model’s validity is demonstrated through actual core experiments, confirming the effectiveness of the single-fracture model while highlighting the need for further refinement of the dual-fracture model. The findings provide scientific support for the exploration and development of granite reservoirs in the South China Sea and establish a foundation for permeability predictions in other complex fractured reservoir systems, thereby advancing the field of fracture permeability assessment.