The core-shell nanostructure of epitaxial Fe3O4 nanocrystals over Ge nuclei showed a large Off/On resistance ratio (∼100), which was the largest value in Fe3O4 materials. The nanocrystals with an average diameter of ∼20 nm were grown epitaxially on Si substrates, whose areal density was high (∼1011 cm−2), and each nanocrystal was isolated from each other. The electrical measurement of the individual isolated nanocrystals by conductive-atomic force microscopy showed the bipolar-type resistive switching in local voltage-current curves, depending on the Fe-O composition. It was also revealed that activation sites for resistive switching were the Fe3O4/Ge interfaces, where electric-field-induced compositional variation caused large resistive changes. This demonstrated the possibility of developing resistance random access memory devices based on ubiquitous materials.