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We investigate the stability of the bi-layer Fe₃O₄/Fe/MgO(0 0 1) films grown epitaxially on MgO(0 0 1) substrates with the layer thickness in the range of 25–100 nm upon 1 MeV Kr⁺ ion irradiation. The layer structure and layer composition of the films before and after ion irradiation were studied by XRR, RBS and RBS-C techniques. The interdiffusion and intermixing was analyzed. No visible change in the RBS spectra was observed upon irradiation with ion fluence below 10¹⁵ Kr cm⁻². The bi-layer structure and the stoichiometric Fe₃O₄ layer on the surface were well preserved after Kr+ ion irradiation at low damage levels, although the strong intermixing implied a large interfacial (FexOy) and (Fe, Mg)Oy layer respective at Fe₃O₄–Fe and Fe–MgO interface. The high ion fluence of 3.8 × 10¹⁶ Kr cm⁻² has induced a complete oxidization of the buffer Fe layer. Under such Kr fluence, the stoichiometry of the Fe₃O₄ surface layer was still preserved indicating its high stability. The entire film contains FexOy -type composition at ion fluence large than 5.0 × 10¹⁶ Kr cm⁻².