Oxidation results in the formation of an oxide film whose properties and structure can be tailored by controlling the oxidation conditions. Reactive molecular dynamics simulations were performed to study thermal oxidation of polycrystalline Al substrates as a function of O2 density and temperature. The structural, chemical, and topological aspects of polycrystalline Al (poly-Al) substrates and oxide films formed upon oxidation were studied. The studies were supported by surface topography and morphology analyses before and after oxidation. An analysis of Al–O atomic pair distribution showed the development of long-range order in the oxide films grown upon exposure to low-density (0.005 g/cm3) and high-density (0.05 g/cm3) O2 gas. The long-range order was more apparent for the high-density environment, as the oxide films formed in low-density O2 gas did not fully cover the poly-Al surface. The dominance of over-coordinated polyhedral units in a tightly packed structure was indicative of medium- and long-range atomic order in the oxide films. The two-phase structure of the oxide was found in the films, with a crystalline phase at the metal/oxide interface and an amorphous phase at the oxide/O2 interface. The combination with topological analyses supported the conclusions of the chemical analysis and enabled us to capture an amorphous-to-crystalline phase transformation in the oxide films with increasing oxygen density and temperature. An important effect of Al surface roughness before oxidation on the behavior of the metal/oxide interface and on the oxide film structure was observed.