Graphene exhibits excellent mechanical properties under atomically thin thickness, which made it very suitable for nanoelectromechanical systems that had high requirements for the thickness of coatings. The epitaxial bilayer graphene on the 4H-SiC (0001) surface presents high stiffness and hardness comparable to diamond. However, due to structural transition occurring at the nanoscale, it is difficult to elucidate reinforcement mechanisms using experimental methods. Here, we applied molecular dynamics simulations to study nanoindentation of epitaxial carbon-film-covered 4H-SiC (0001) surfaces. Because a weak interaction potential existed between graphene layers at indentation depth (h < 0.8 Å) that far smaller than interlayer distance, the epitaxial bilayer graphene does not allow the 4H-SiC to exceed its intrinsic stiffness. When the indentation depth h ≥6.45 Å, the sp3 hybridized bonds formed on the interlayer of graphene, which leads to fewer amorphous atoms in the sample of 4H-SiC and exhibits stronger stiffness, in comparison with bare 4H-SiC. This strongly suggests the existence of sp3 bonds contributing to the surface strengthening. Meanwhile, we found that the comprehensive mechanical properties of nanocomposites with hydrogenated diamond-like films were superior to those of nanocomposites with other carbon films at high temperatures.