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Controlled oxidation of graphitic materials offers a route to tune their electronic and transport properties, yet the mechanisms underlying the evolution of oxygen clusters and the formation of carbon vacancies remain insufficiently understood. Here, we report a density functional theory investigation of oxygen cluster transformation in graphene. We reveal that for several O atom configurations, circular clusters are energetically more favorable than linear chains. However, the predominant formation of linear chains is attributed to their simpler stepwise growth and substantial reorganization barriers (up to 1.6 eV). We further identify reaction pathways for the formation of carbon vacancies, showing that epoxy migration toward the cluster core provides a more favorable route to pore formation than ether migration, which faces migration barriers exceeding 2.0 eV in larger clusters. Overall, our findings offer mechanistic insight into the evolution of oxidized graphene into nanoporous structures, informing the design of controlled functionalization strategies for 2D materials.