Controlling wrinkle nanostructures of two-dimensional materials is critical for optimizing the material properties and device performance. In this study, we demonstrated the in situ synthesis of large-area MoS2 wrinkles on graphene by chemical-vapor-deposition-assisted sulfurization, and investigated the influence of graphene thickness and grain structures on the feature dimensions of MoS2 wrinkle nanostructures. The height, width, and overall surface roughness of the MoS2 wrinkles diminish as the number of graphene layers increases, which was further verified by determining the binding energy of graphene layers by density functional theory calculations. Furthermore, the feature dimensions of MoS2 wrinkle nanostructures were also influenced by graphene domain boundaries because of the difference in graphene nucleation density. This may be attributed to the influence of the mechanical properties of graphene substrates on the overall feature dimensions of MoS2 wrinkles, which are directly correlated with the interfacial adhesion energy. We believe that our findings may contribute toward the controllable synthesis of MoS2 wrinkle nanostructures and other two-dimensional materials used for high-performance devices.