To investigate the mechanism of interaction between root-soil composites and rock interfaces in the ecological protection of rocky slopes, physical models of interfaces were established, considering different plant species, types of soil for slope protection, and degrees of rock weathering. Under natural stress conditions, direct shear tests on the root-soil-rock interfaces were conducted. The variation patterns of shear strength and shear displacement at the interfaces were revealed, and the influence mechanisms of plant root morphology, types of protective soil, and rock weathering degree on the shear strength of the interfaces were analyzed. The results indicate that plant roots, penetrating through the slope protection soil and into the bedrock fissures, significantly enhance the shear strength of the soil in the shear zone and the anti-slip capacity of the soil-rock interface, thereby improving the overall cohesion between the slope protection soil and the rock. The shear strength of the interface is positively correlated with the vertical extension of plant roots and the degree of rock weathering. Compared to scenarios without plants, the planting of vetiver grass increased the peak shear strength by 53.9%, and under highly weathered bedrock conditions, the peak strength increased by 22.4%. Compared to ordinary soil, substrate soil containing binders and aggregating agents significantly improved the shear performance of the soil, increasing the peak shear strength of the interface by 20.1%.