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The commercialization of GaN-based Schottky barrier diodes in middle- and high- voltage applications still faces many challenges, in which the lack of an effective selective area p-type doping method is one of the main obstacles. This paper proposes novel vertical GaN-based Schottky diodes with trench MIS structure and an embedded p-GaN protection layer (junction-trench MIS barrier Schottky diodes, J-TMBS). The trench structure and lateral p-n junctions can be achieved by selectively etching the very thin p-GaN and then regrowing n-GaN. Therefore, the fabrication technology avoids the selective area p-type doping process, and the dry etching damage and poor sidewall regrowth interface issue, which are serious in GaN Merged pn/Schottky (MPS) diodes, can also be alleviated for the proposed J-TMBS. Compared with the optimized GaN trench MIS barrier Schottky (TMBS) diodes, the surge current capability and dielectric reliability of the proposed J-TMBS are significantly improved (the electric field of the dielectric layer and maximum lattice temperature under the surge test can be reduced by 448% and 202%, respectively). In addition, the specific on-resistance (Ron,sp) and breakdown voltage remain basically unchanged compared with TMBS. Compared with the optimized GaN MPS diodes, the proposed structure improves the specific on-resistance by 17.2% benefiting from the reduced area of the JFET region without degrading the reverse I–V characteristics and surge current capability. The proposed J-TMBS exhibits potential in practical high voltage (>600 V) application of GaN Schottky power diodes.