The present invention relates to a method of manufacturing a nano transistor. The present invention manufactures the nano transistor without changing a conventional method of forming the nano transistor formed on a SOI substrate. Further, the present invention includes forming a N well and a P well at giving regions of an underlying silicon substrate so that a given voltage can be individually applied to a NMOS transistor and a PMOS transistor. Therefore, the present invention can control the threshold voltage to prevent an increase of the leakage current.