A method of the production of a nanoparticle dispersed composite material capable of controlling a particle size and a three dimensional arrangement of the nanoparticles is provided. The method of the production of a nanoparticle dispersed composite material of the present invention includes a step (a) of arranging a plurality of core fine particle-protein complexes having a core fine particle, which comprises an inorganic material, internally included within a protein on the top surface of a substrate, a step (b) of removing the protein, a step (c) of conducting ion implantation from the top surface of the substrate, and a step (d) of forming nanoparticles including the ion implanted by the ion implantation as a raw material, inside of the substrate.