A method of producing a structure containing a phase-separated structure, including forming a layer containing a block copolymer on a substrate; applying a top coat material to the layer containing the block copolymer to form a top coat film; and subjecting the layer including the block copolymer having the top coat film formed thereon to annealing treatment so as to conduct a phase separation of the layer, the top coat material including an organic solvent component and a polymeric compound containing a structural unit having either a dicarboxylic acid or a salt of a dicarboxylic acid, and the organic solvent component containing water and an alcohol having 3 or more carbon atoms.