In this study, we characterized Fe 3 O 4 (001) films using scanning tunneling microscopy/spectroscopy (STM/STS). On the film surfaces, individual iron atoms and (√ 2× √ 2)R45 • reconstructed structures were observed by STM. The STS results showed the higher local density of states just below the Fermi level of narrow sections than wide ones of the surface reconstruction perpendicular to the iron rows. Periodical density of states modulations reproducing this electronic structure were clearly observed by the differential tunneling conductance map. These experimental results revealed the presence of subsurface charge ordering of Fe 2+-Fe 2+ and Fe 3+-Fe 3+ dimers, as proposed in previous density functional theory studies.