Based on a systematic study of gas-phase silicon oxide clusters and the subsequent interesting findings such as the gas-phase favorable composition and distinctive features in reactivity of the different silicon oxide clusters, we have elucidated the mechanism of oxide-assisted nucleation of silicon nanostructures. In the mechanism, a part of the highly reactive Si atoms in the silicon suboxide clusters deposited on the substrate would form bonds with the substrate atoms, anchoring the cluster to the substrate. The remaining reactive Si atoms facing outwards from the substrate are exposed to the vapor, favoring further stacking of silicon oxide clusters. They act as the nuclei to absorb reactive silicon oxide clusters and facilitate the formation of the Si nanowires with a certain crystalline orientation. We expect that the present oxide-assisted formation mechanism of nanostructures may be applicable to a wide range of materials synthesis or design.