Despite some successful studies of two-phase or unsaturated flows in ideal smooth-walled fractures, the more realistic issues regarding fundamentals of two-phase interactions in rough-walled fractures are still poorly understood. In this study, we suggest a new approach to describe relative permeability behavior in rough-walled fractures based on experimental observations of two-phase flow structures. This approach lumps the microscale physical mechanism (viscous and capillary forces) into an apparent observable parameter, the channel tortuosity, which was found to dominate the reduction of the relative permeabilities from the values that would be expected based on the linear X curve (i.e., relative permeability equals saturation). Two analog fractures, the homogeneously rough-walled and randomly rough-walled fractures, combined with a smooth-walled fracture investigated previously were studied to represent distinct surface geometry and heterogeneity. The uncertainty and quality of measured relative permeabilities in the fractures were discussed in the aspects of high-resolution relative permeability and different averaging techniques. The experimental results from these three fractures could be described successfully by the proposed approach. Furthermore, we found that the magnitude of the channel tortuosity increases when the heterogeneity of the fracture surface increases. We also showed that the rates' (velocities) effects on flow structures within the experimental ranges were insignificant. Generalizing from channel tortuosities occurring in these three fractures, we were able to derive empirical, tortuous channel models. These models represent the current experimental data as well as observations from earlier studies with good agreement.