The atomistic interface structure between β-FeSi2 and Si substrate was investigated by cross-sectional scanning transmission electron microscopy and density functional theory calculations (DFT). A high quality single crystalline β-FeSi2 film was epitaxialy grown on Si(001) substrate. We demonstrate that the β-FeSi2(100) plane is bonded to the Si(001) plane with two Si dimers per unit cell. With such interface structure, DFT band calculations reveal that metallic electronic states are localized at the interface. This finding implies the presence of two dimensional electronic states at the interface of β-FeSi2/Si(001), which may have potential applications in silicon-based electronic devices.