The concrete–rock interfacial transition zone (ITZ) is generally considered the weak layer in hydraulic engineering, for it is more permeable than the intact concrete or rocks. The water permeability of the ITZ is a critical parameter concerned with structural safety and durability. However, the permeability and pore structure of the ITZ has not been investigated previously, and the mathematical model of ITZ permeability has not been established. This study performed multi-scale experiments on the concrete–rock ITZ with various rock types (limestone, granite, and sandstone). A series of quantitative and qualitative analysis techniques, including NMR, SEM-EDS, and XRD, characterize the ITZ pore structures. The controlled constant flow method was used to determine the permeability of the concrete, rock, and ITZ. The mathematical model of ITZ permeability was proposed using the fractal theory. The consistency between the experimental data and the proposed model indicates the reliability of this study. The results of the experiment show that ITZ permeability is between 4.08 × 10⁻¹⁸ m² and 5.74 × 10⁻¹⁸ m². The results of the experiment and the proposed model could determine ITZ permeability in hydraulic structure safety and durability analysis.