ReaxFF-based molecular dynamics was used to demonstrate the limited coating effect of pristine graphene in protecting a typical Ni(111) substrate against hyperthermal oxygen species. Under 10-eV O2 and O3 molecules, graphene remained intact, and served as a protective coating by preventing the diffusion of molecules towards underlying Ni(111). By increasing the initial energy of incident species to 20 and 30 eV, graphene failed to provide efficient protection, offering protection degrees of 53.16 and 40.87% against O2, and 55.12 and 47.78% against O3. As opposed to O2 and O3, 10-eV O exposure led to a low protection degree of 58.95%, decreasing to 21.98%, and switching to 6.20% anti-protection when the initial energy increased to 20 and 30 eV. Through the detailed analysis of simulated trajectories, a three-stage oxidation process was proposed, elucidating the mechanism for these low protection degrees. On the basis of the proposed mechanism, the graphene’s coating effect is limited by the formation and growth of defects on graphene, enabling atomic diffusion across the graphene-Ni(111) interface, and leading to NiO formation over the damaged regions of graphene. The structural analysis then confirmed graphene’s transformation from a crystalline to a highly disordered carbon phase decorated by an amorphous NiO phase.