Polymer grouting materials are widely used in the trenchless rehabilitation of underground pipe networks and infrastructures. Numerous publications focused on the mechanical properties of the composite's interface, which is critical for the stability and strength of composite structures. However, there is a scarcity of reports on the microscopic characterization and interactive mechanisms of polymer-bentonite system. In this paper, a microscopic combination interface model of polymer-bentonite was constructed based on the molecular dynamics simulation method, and the interfacial shear mechanical properties were investigated under different working conditions. The results show that the shear strength of the polymer-bentonite interface increases with the increase of shear rate and normal stress, which is consistent with the experimental results. The application of normal stress leads to a decrease in the van der Waals gap at the interface and an increase in the density of the dense interface, thus increasing the shear strength of the interface. In addition, the shear strength of the interface in the presence of defects on the surface of the clay crystals is determined by the nonbonding interaction potential energy together with the roughness. As the shear rate increases, shear thinning occurs at the polymer-bentonite interface, and the effect of roughness on the interfacial shear properties gradually decreases. This paper reveals the mechanical properties of the polymer-bentonite interface under the influence of different factors from a microscopic point of view.