1H,1H,2H,2H-Perfluorodecyltriethoxysilane (PFDTES) is the most widely used coating material with low surface energy and has the potential to be used as a dust-mitigating coating material during lunar landing missions. Graphene can be added to the PFDTES matrix to improve its mechanical properties. In this study, molecular dynamics simulations were performed to investigate the interfacial shear strength and friction mechanism between the PFDTES matrix and graphene. A systematic molecular dynamics (MD) simulation has been performed to calculate the interfacial shear strength of the PFDTES–graphene interface with considering the effect of graphene sliding velocity and vacancy defect density. For a pristine graphene layer with a size of 10 nm × 10 nm, the interfacial force between graphene and the PFDTES matrix is around 3 nN. Like other polymeric materials, the interfacial shear force exhibited stick–slip behavior under loading. The interfacial shear force will start to increase after the graphene starts sliding against the PFDTES matrix and reaches a stable plateau in a very short distance. It has been found that the influence of the interfacial shear strength from the sliding velocity of graphene is minimal. However, a significant increase in the interfacial shear strength has been observed after the graphene defect density increased; i.e., the magnitude of the shear force increased from 3 nN to around 14 nN after the defect density increased from 0% for pristine graphene to 40%. It has been found that vacancy defects will increase the fluctuation in the interfacial shear force, and it is due to not only the increased roughness near defects but also the stretched bonds in graphene under loading according to the distribution of the bond length. This study concluded that interfacial stick–slip behavior also exists in the PFDTES–graphene interface, and vacancy defects will have a significant improvement in the interfacial shear strength.