An AlGaN/GaN HEMT based on fluorinated graphene passivation and a manufacturing method thereof. Monolayer graphene (108) is transferred to an AlGaN (104) surface, is treated by using fluoride ions and then is insulated to thereby replace a conventional nitride passivation layer. Then, a high-k material (109) is grown on the graphene (108), and the high-k material (109) and the graphene (108) are jointly used as a gate dielectric for preparing an AlGaN/GaN metal-insulator-semiconductor (MIS) HEMT. Compared with the traditional passivation structure, the graphene (108) has the advantages of small physical thickness (sub-nanometer scale) and low additional threshold voltage. The structure and the method are simple, the effect is remarkable and the application prospect in technical fields of microelectronics and solid-state electronics is wide.