There is provided a method of manufacturing a nano-wire using a crystal structure. In the method of manufacturing a nano-wire, a crystal grain having a plurality of crystal faces is used as a seed, and a crystal growing material having a lattice constant difference within a predetermined range is deposited on the crystal grain, thereby allowing the nano-wire to grow from at least one of the crystal faces. Therefore, it is possible to give the positional selectivity with a simple process using a principle of crystal growth and to generate a nano-structure such as a nano-wire, etc. having good crystallinity. Further, it is possible to generate a different-kind junction structure having various shapes by adjusting a feature of a crystal used as a seed.