A systematic investigation of the thickness and oxygen pressure dependence for the structural properties of ultra-thin epitaxial magnetite (Fe3O4) films has been carried out; for such films, the structural properties generally differ from those for the bulk when the thickness ⩽10 nm. Iron oxide ultra-thin films with thicknesses varying from 3 nm to 20 nm were grown on MgO (0 0 1) substrates using molecular beam epitaxy under different oxygen pressures ranging from 1 × 10(-7) torr to 1 × 10(-5) torr. The crystallographic and electronic structures of the films were characterized using low energy electron diffraction (LEED) and x-ray photoemission spectroscopy (XPS), respectively. The quality of the epitaxial Fe3O4 ultra-thin films was judged by magnetic measurements of the Verwey transition, along with complementary XPS spectra. It was observed that under the same growth conditions the stoichiometry of ultra-thin films under 10 nm transforms from the Fe3O4 phase to the FeO phase. In this work, a phase diagram based on thickness and oxygen pressure has been constructed to explain the structural phase transformation. It was found that high-quality magnetite films with thicknesses ⩽20 nm formed within a narrow range of oxygen pressure. An optimal and controlled growth process is a crucial requirement for the accurate study of the magnetic and electronic properties for ultra-thin Fe3O4 films. Furthermore, these results are significant because they may indicate a general trend in the growth of other oxide films, which has not been previously observed or considered.