The invention is applicable to the technical field of semiconductor devices, and particularly relates to a GaN-based heterojunction field effect transistor and a manufacturing method thereof. The transistor sequentially comprises a substrate, a nucleating layer, a buffer layer, a channel layer, an insertion layer, a barrier layer, a source electrode, a grid electrode and a drain electrode from bottom to top, wherein the source electrode, the grid electrode and the drain electrode are arranged on the barrier layer. Passivation layers are arranged between the source electrode and the grid electrode and between the grid electrode and the drain electrode on the barrier layer. Field plates are arranged on the passivation layers. The forming material of the barrier layer includes: B (Al, Ga, In)N. The forbidden band width of the barrier layer is larger than the forbidden band width of the channel layer and smaller than the forbidden band width of the insertion layer. A heterojunction interface formed by the barrier layer made of the B (Al, Ga, In) N materials is large in band gap difference. The barrier layer has super-large polarization field intensity, very high two-dimensional electron gas concentration can be obtained, and the high-frequency requirement of a device is met. Through the field plates, the electric field peak value of the grid edge can be reduced, the channel electric field distribution uniformity of the device is improved, the breakdown voltage of the device is increased and the high-voltage requirements are met.