The soil-structural interface is involved in many geotechnical engineering problems. Previous investigations have mainly relied on the macro-scale observations from laboratory experiment. However, soil is a type of granular material, and recent research works reveal that the macroscopic responses of granular materials originate from the evolution of the microstructures. Therefore, to understand well the shearing behavior of soil adjacent to an artificial interface, it is necessary to explore this problem on the particle scale. In this study, an interface shear test is modeled using the three-dimensional discrete element method. Five shear boxes of distinct size are modeled to verify the scale effect. According to the comparison between the interface shear tests in terms of computation time, shear strength measured on the interface and volumetric strain of the specimen, an interface shear box containing 14,000 particles is sufficient for this study. Then, a series of three-dimensional interface shear tests with distinct normalized roughness “Rn” is modeled. The results show that (1) two failure modes exist in an interface shear test, elastic-perfectly plastic for a smooth surface and stress softening observed for a rough surface, and (2) the shear strength of the soil-structural interface increases with the increasing of the roughness of the interface. The displacement field is obtained by interpolating the movement of each particle. The field of ux (displacement in the direction of shearing) indicates that a narrow zone of intense shearing deformation, called the shear band, emerges from the contact interface and expands during the shearing process. A discontinuous feature is characterized after the shear band appears.