The invention provides a GaN-based vertical power transistor device and a fabrication method thereof. The GaN-based vertical power transistor device comprises an N-type GaN substrate, an N-type GaN epitaxial layer, a Al(In, Ga)N back barrier layer, a thin barrier layer Al(In, Ga)N/GaN heterojunction structure, a passivation layer, a gate, a source and a drain, wherein the N-type GaN epitaxial layer is formed on the N-type GaN substrate, the Al(In, Ga)N back barrier layer is formed on the N-type GaN substrate, the thin barrier layer Al(In, Ga)N/GaN heterojunction structure is formed on the Al(In, Ga)N back barrier layer, the passivation layer, the gate and the source are formed on the thin barrier layer Al(In, Ga)N/GaN heterojunction structure, and the drain is formed on the N-type GaN substrate. With the GaN-based vertical power transistor device and the fabrication method thereof, the process difficulty of the GaN-based vertical power transistor is effectively reduced, so that the GaN-based vertical power transistor device is compatible with a process of a conventional GaN-based transverse device, and the application of the GaN-based vertical power transistor in conversion of higher current and power is promoted.