<p>The permeability of soil–structure interfaces is often greater than that of homogeneous soil, which can easily lead to engineering seepage failure. However, the seepage characteristics and mechanisms of such interfaces remain unclear. In this study, laboratory seepage tests were conducted to investigate the effects of clay content, degree of compaction, confining pressure, and structural surface roughness on the seepage characteristics of the interface. The variation law of the critical hydraulic gradient at the interface was also quantified. Additionally, CFD–DEM simulations and geometric analysis were used to explain the mechanisms underlying the enhanced permeability of the interface. The results show that the interface seepage process comprises three stages: stable seepage, transitional seepage, and failure seepage. Interface permeability is positively correlated with clay content, compaction, and confining pressure, and negatively correlated with surface roughness. The porosity and seepage velocity of the interface soil are greater than those of homogeneous soil, with particles close to the structural surface being the first to be displaced by water flow. This phenomenon is primarily attributed to the constraint effect of the structure, which alters the arrangement of soil particles and increases the porosity of the interface soil.</p>