Oxidation of graphitic materials has been studied for more than a century to synthesize materials such as graphene oxide, nanoporous graphene, and to cut or unzip carbon nanotubes. However, the understanding of the early stages of oxidation is limited to theoretical studies, and experimental validation has been elusive. This is due to (i) challenging sample preparation for characterization because of the presence of highly mobile and reactive epoxy groups formed during oxidation, and (ii) gasification of the functional groups during imaging with atomic resolution, e.g., by transmission electron microscopy. Herein, we utilize a low-temperature scanning tunneling microscope (LT-STM) operating at 4 K to solve the structure of epoxy clusters form upon oxidation. Three distinct nanostructures corresponding to three stages of evolution of vacancy defects are found by quantitatively verifying the experimental data by the van der Waals density functional theory. The smallest cluster is a cyclic epoxy trimer. Their observation validates the theoretical prediction that epoxy trimers minimize the energy in the cyclic structure. The trimers grow into honeycomb superstructures to form larger clusters (1–3 nm). Vacancy defects evolve only in the larger clusters (2–3 nm) in the middle of the cluster, highlighting the role of lattice strain in the generation of vacancies. Semiquinone groups are also present and are assigned at the carbon edge in the vacancy defects. Upon heating to 800 °C, we observe cluster-free vacancy defects resulting from the loss of the entire epoxy population, indicating a reversible functionalization of epoxy groups.