A GaN-based superjunction vertical power transistor and a manufacturing method thereof. The transistor includes: a N−-GaN layer; a first P-GaN layer as a current blocking layer, formed on the N−-GaN layer and having a gate region window; and a thin barrier Al(In, Ga)N/GaN heterostructure conformally formed on the current blocking layer and filling the bottom and one or more sidewalls of the gate region window, wherein the N−-GaN layer has an etched groove completely or partially filled with a second P-type GaN layer, an N+-GaN layer is formed under the second P-type GaN layer, and the N+-GaN layer is in direct contact with the second P-type GaN layer and the N−-GaN layer to form a superjunction composite structure.