The invention discloses a method of manufacturing GaN-based field-effect transistors, which includes steps of surface-finishing a GaN-based material layer, depositing a silicon oxide protective layer,forming lithographic alignment marks via lithography, dry-etching the silicon oxide protective layer, evaporating marked metal, forming source-drain patterns via lithography, dry-etching the siliconoxide protective layer, evaporating source-drain metal, annealing alloy at high temperature, forming shielding active region patterns via lithography, forming active region isolation via ion implantation, then wet-etching the silicon oxide protective layer, depositing silicon nitride on the surface of the GaN-based material, passivating field effect transistors, forming grids via electron-beam direct writing or optical lithography, dry-etching the silicon nitride and the GaN-based material layer at the top to form a gate-recessed structure, evaporating gate metal and metal wiring. The method of manufacturing GaN-based field-effect transistors avoids the surface of the GaN-based material being exposed in air, prevents the surface of the GaN-based material from being polluted during fabrication process, and inhibits current collapse effect of AlGaN / GaN HEMTs.