Iron (Fe) nanocrystals (NCs) were epitaxially grown on silicon (Si) substrates, where interfacial alloying of Fe and Si (silicidation) was prevented using an ultrathin SiO2 film. Nanowindows (NWs) composed of Si and germanium (Ge) were introduced into this SiO2 layer. The crystallographic arrangement of the Si substrates was conveyed though the NWs, while Fe and Si atoms were not intermixed. Reactions between the epitaxial Fe NCs and Si substrate in the presence of oxygen gas were also investigated. Oxygen atoms facilitated the diffusion of Fe from NCs to Si substrates mainly through Si NWs. As a result, increase of oxygen concentration led to Si oxidation near the interface. This means Fe NCs played a role like a catalysis for Si oxidation. The interfacial reaction was changed drastically by control of nanometer-sized interfaces using Ge NWs in the ultrathin SiO2 films.