A heterojunction semiconductor device comprises a substrate; a second barrier layer is disposed on the second channel layer and a second channel is formed; a trench gate structure is disposed in the second barrier layer; the trench gate structure is embedded into the second barrier layer and is composed of a gate medium and a gate metal located in the gate medium; an isolation layer is disposed in the second channel layer and separates the second channel layer into an upper layer and a lower layer; a first barrier layer is disposed between the lower layer of the second channel layer and the first channel layer and a first channel is formed; a bottom of the metal drain is flush with a bottom of the first barrier layer; and a first metal source is disposed between the second metal source and the first channel layer.