A method of manufacturing a nano membrane structure includes preparing a temporary structure having a substrate in which a through-hole is formed in a central portion, and a nano membrane including silicon nitride (SiN), that covers the through-hole on the substrate, and including a central area formed on the through-hole, and a peripheral area formed on the substrate. The method includes preparing an insulating support member including at least one of silicon and a compound containing silicon, and in which a micropore is formed in a central portion, forming a complex structure by performing a hydrophilic surface processing of a surface of the nano membrane and one surface of the insulating support member and by bonding the temporary structure and the insulating support member so that at least a portion of the central area of the nano membrane and the micropore face, and removing the substrate from the complex structure.