A method of manufacturing a vertical structure light emitting diode device, the method including: sequentially forming a first conductivity type III-V group compound semiconductor layer, an active layer, and a second conductivity type III-V group compound semiconductor layer on a substrate for growth; bonding a conductive substrate to the second conductivity type III-V group compound semiconductor layer; removing the substrate for growth from the first conductivity type III-V group compound semiconductor layer; and forming an electrode on an exposed portion of the first conductive III-V group compound semiconductor layer due to the removing the substrate for growth, wherein the bonding a conductive substrate comprises partially heating a metal bonding layer by applying microwaves to a bonding interface while bringing the metal bonding layer into contact with the bonding interface.