The invention discloses a hetetrostructure field effect diode and a manufacturing method thereof. The hetetrostructure field effect diode comprises a substrate as well as an insulation high-resistance semiconductor and a wide bandgap hetetrostructure barrier layer which are sequentially arranged on the substrate, wherein the insulation high-resistance semiconductor and the wide bandgap hetetrostructure barrier layer form a two-dimensional electron gas hetetrostructure epitaxial layer, an isolated table board is formed at the top of the insulation high-resistance semiconductor and the wide bandgap hetetrostructure barrier layer, an insulating medium layer is formed on the isolated table board, a cathode electrode and an anode electrode which are contacted with the wide bandgap hetetrostructure barrier layer are respectively formed on the insulating medium layer, wherein one part of the anode electrode is arranged on the wide bandgap hetetrostructure barrier layer, the other part of the anode electrode is arranged on the insulating medium layer to form a diode anode provided with a Schottky-MIS (metal-insulator-semiconductor) dual-structure electrode, and the anode electrode is made from a low-work function metal. According to the invention, the characteristics of low forward on voltage, low reverse leakage current and high reverse blocking voltage can be realized, thus, the method in the invention is applicable to manufacturing of a power type GaN-base hetetrostructure field effect diode.