Ultra-deep fractured-cave carbonate reservoirs are buried at great depths, with high stresses, and possess complex and diverse storage spaces. Fluid flow and seepage coexist, making the characterization of reservoir connectivity challenging. Accurate characterization of reservoir connectivity is crucial for identifying oil and gas enrichment areas, predicting reserves precisely, optimizing well patterns, and planning well locations. Therefore, this study focuses on the ultra-deep fractured-cave carbonate reservoirs in the Fuman Oil Field of the Tarim Basin. Considering the effect of fluid-solid coupling, a coupled mathematical model of stress seepage and free flow in fractured-cave reservoirs was established. A systematic study on the connectivity of ultra-deep fractured-cave carbonate reservoirs was conducted using a combination of rock permeability evolution experiments and numerical simulations. The research results indicate that with the increase of confining stress and axial stress, rock permeability gradually decreases, leading to weakened rock connectivity. Under low confining stress conditions, axial stress significantly affects rock permeability and connectivity. As the fracture aperture and angle increase, reservoir connectivity gradually improves. Fracture-connected caves can significantly enhance reservoir connectivity. The fluid flow rate and equivalent permeability increase with the increase in cave volume, which greatly improves reservoir connectivity. However, simply increasing the number of caves weakens the free flow (Stokes) effect, resulting in a less significant improvement in reservoir connectivity. The research findings provide technical support for the precise evaluation of deep carbonate reservoirs and enhance the efficiency of oil and gas exploration and development.