It is to provide an inorganic thin film of titanium dioxide or the like which is controlled at the nanoscale and a three-dimensional structure of a functional material such as semiconductor nanoparticles. A three-dimensional structure of an inorganic material is manufactured by introducing onto a surface of an inorganic substrate ferritin presenting on its surface a plurality of inorganic material-binding peptides; binding the ferritin in a monolayer onto the inorganic substrate; introducing an inorganic material onto the ferritin which is bound in a monolayer, while the inorganic material-binding peptides is having a binding and/or biomineralization ability for the inorganic material; forming a biomineral layer utilizing the biomineralization ability of the inorganic material-binding peptides; and subsequently repeating one or more times the steps (a) and (b) of a multilayering operation: (a) introducing onto the biomineral layer thus formed the ferritin having a binding ability to the biomineral layer, and binding the ferritin in a monolayer onto the biomineral layer; (b) introducing the inorganic material onto the surface of the ferritin which is bound in a monolayer, and forming a biomineral layer.