The invention discloses an organic modified nanometer complex oxide material and a preparation method thereof. The SiO2 microsphere is taken as a substrate, an inorganic metal oxide is embedded in the bulk phase of the SiO2 microsphere and an organic group is connected to the surface of the inorganic metal oxide; the organic modified nanometer complex oxide material is expressed in a general formula MeOg-SiO2, wherein Me is short for Metal, and Og is short for Organicgroup; and Me is one or more of Co, Mn, Cu, Fe, V, Ti, Cr, Ni, Zn, Zr and Al and Og is one or more of methyl, ethyl, propyl, vinyl, chloroallyl, naphthyl, phenyl, trifluoropropyl, fluorophenyl and pentafluorophenyl. The operational process is simple and easy to control. Since the metallic ion and the organic group are respectively introduced on the bulk phase and the surface of the SiO2 simultaneously, the invention has the broad prospect on the application aspects of nano-devices and functional material.