The invention discloses a super-junction gallium oxide transistor based on a heterojunction and a manufacturing method and application thereof, and belongs to the technical field of semiconductor materials and devices. The super-junction gallium oxide transistor comprises a super-junction structure, wherein the super-junction structure is formed in a gallium oxide drift region of the transistor, and gallium oxide-based heterogeneous PN junctions are formed in a staggered mode. The present invention forms heterogeneous super junction structure in the drift region of gallium oxide channel, Correcting the electric field distribution mode of the gallium oxide drift region, The peak electric field at the edge of the grid is effectively reduced, The electric field of the drift region is diffused from the edge of the grid electrode to the direction of the drain electrode, so that the restriction relation between the breakdown voltage and the on-resistance of the oxidant transistor is broken through, higher breakdown voltage and lower on-resistance can be obtained, a gallium oxide device with excellent performance is obtained, and a solid foundation is laid for wide application of the gallium oxide device in the field of electronic power.