A manufacturing method of a microstructure which enables production of a deep and narrow microstructure in a GaN semiconductor with high precision is provided. The manufacturing method of a microstructure for forming a microscopic structure in a semiconductor has a configuration having a first step of forming a first GaN semiconductor layer on a substrate, a second step of forming a first hole by using etching on the first GaN semiconductor layer formed in the first narrow, and a third step of performing heat-treatment at a temperature from 850° C. to 950° C. inclusive under a gas atmosphere including nitrogen, in order to form a second narrow in which a diameter of the first hole h formed in the second step is made narrower than the diameter of the first hole in an in-plane direction of the substrate.