A method of producing a structure containing a phase-separated structure, including: forming a layer including a neutralization film on a substrate; forming a layer containing a block copolymer on the layer including the neutralization film, the PA block and PB block being mutually bonded in the block copolymer, and the PB block including a structural unit other than a structural unit constituting the PA block; and subjecting the layer containing the block copolymer to an annealing treatment, such that, in the case where a surface free energy of the PA block, a surface free energy of the PB block and a surface free energy of the neutralization film are represented by a coordinate point A of the PA block, a coordinate point B of the PB block and a coordinate point N of the neutralization film, respectively in the plane of coordinates, the coordinate point N of the neutralization film is within the predetermined range.