It is an object to provide a microstructure having cylindrical microdomains oriented in the film thickness direction and arranged in a regular pattern, for which a microphase separation phenomenon of a block copolymer is utilized. The process for producing the microstructure includes 2 steps; the first step for arranging, on a substrate (40), a polymer layer at least containing a block copolymer having a first block which constitutes a continuous phase (10) of the microstructure (30) and a second block which constitutes microdomains (20) dispersed in the continuous phase (10) and oriented in the thickness direction; and second step for thermally treating the substrate (40) at a neutral temperature (Tn), at which a first material (A) and second material (B) which constitute the respective first and second blocks have substantially the same interfacial tension with the substrate (40) surface (X).