Reducing the friction and wear of nanodevices are the key to improve the performance of micro/nanoelectromechanical systems (M/NMES). In this paper, a gallium nitride (GaN) substrate coated with a single layer of graphene was constructed using molecular dynamics (MD) simulation, and then scratched with a diamond tip under a constant load. The results showed that graphene can improve the abrasion resistance and hardness of the substrate, and reduce surface wear, temperature, potential energy, and subsurface damage. However, the effect of graphene to inhibit the generation of dislocations within the substrate was not obvious. In addition, the substrate surface exhibited super-lubrication at low load scratching. As the load increased, the friction and wear on the substrate surface increased. The application of graphene can extend the load range over which the substrate undergoes full elastic deformation, which means a greater range of super-lubrication. The protective and lubricating effects of graphene provide guidance for the design of GaN-based nanodevices.