High quality epitaxial Fe3O4, NiO and a series of Fe1−xNixOy (0<x<1) thin films have been fabricated by molecular beam epitaxy. In situ reflection high energy electron diffraction (RHEED), ex situ X-ray diffraction (XRD), and X-ray absorption spectroscopy (XAS) studies have been carried out. It was observed that the crystal structure of all the Fe1−xNixOy films studied resemble that of the inverse spinel Fe3O4. The lattice spacing along the perpendicular direction as a function of x shows a minimum at x=0.5 instead of a linear variation indicating that the structures are different from a bulk ferrite Fe2NiO4-like phase. The XAS results are consistent with XRD results and further identify the cation distribution in Fe1−xNixOy system as x varies. The mechanism of the formation of the metastable phase and its implication on the magnetic properties of these Fe–Ni–O films are briefly discussed.