A microstructure manufacturing method includes forming a first insulating film on an Si substrate, exposing an Si surface by removing a part of the first insulating film, forming a recessed portion by etching the Si substrate from the exposed Si surface, forming a second insulating film on a sidewall and a bottom of the recessed portion, forming an Si exposed surface by removing at least a part of the second insulating film formed on the bottom of the recessed portion, and filling the recessed portion with a metal from the Si exposed surface by electrolytic plating.