Shear characteristic of base material soil-rock interface plays a key role for long-term stability of ecological slope protection system. Related research on this can provide necessary basis and guidance for resolving the substrate failure and improving the ecological protection technology. The self-made in-situ shear apparatus is used in the field shear tests of 4 groups of base material soil-rock interfaces with different roughnesses. Experimental results show that shear stress-displacement of the base material soil-rock interface is characterized by typical shear softening, including 4 stages of initial linear elastic deformation, elastic plastic deformation, the post-peak softening and residual shear deformation. Under the test conditions, it is found that the peak shear strength increases fast when the arithmetic average deviation of asperity (Ra) is about less than 4 mm. For the higher Ra, the increasing gradient shows a slower trend. Residual shear strength, peak shear displacement and shear displacement stepping to the residual stage show the nearly linear positive correlation with Ra. Therefore, for a specific implementation of ecological slope protection, the reasonable control of slope surface roughness will contribute to increasing the peak and residual shear strength of soil-rock interface, so as to improve the deformation performance and the long-term stability of the protection system.