The invention relates to the semiconductor device field, discloses a GaN MISFET of high quality MIS grid structure and a manufacturing method thereof and especially relates to an improved method of a MIS interface. The device comprises a substrate, an epitaxial layer, a grid dielectric layer, a source electrode, a drain electrode and a grid electrode, wherein the epitaxial layer, the grid dielectric layer, the source electrode, the drain electrode and the grid electrode are growth on the substrate. The epitaxial layer comprises a first epitaxial growth stress buffer layer, a GaN epitaxial layer and an AIN thin layer. On the epitaxial layer, an area is selected to grow a secondary epitaxial layer and a groove channel is formed. And then, the grid dielectric layer is deposited, grid metal covers the groove channel grid dielectric layer, and two ends of the grid are covered by metal so as to form the source electrode and the drain electrode. The device structure and a manufacturing technology are simple and reliable, the MIS grid interface with high quality can be formed and performance of the GaN MISFET device is increased. The method is important for reducing a channel resistance and improving a threshold voltage stability problem.