The invention discloses a system and a method for treating dioxin in incineration fly ash through a continuous microwave hydrothermal method. The system for treating dioxin in incineration fly ash through the continuous microwave hydrothermal method comprises a heat exchange device, a buffer stirring tank, a circulating pump and a microwave reaction device. The microwave reaction device comprises a microwave safety shielding unit, a slurry circulating unit, a microwave irradiation unit and a control unit; a feed port of the slurry circulating unit is connected with the buffer stirring tank, and a discharge port of the slurry circulating unit is connected with a heat exchange device; and a circulation loop communicated with the buffer stirring tank is arranged on the pipeline between the microwave reaction device and the heat exchange device. A high-parameter microwave treatment technology is implanted on the basis of traditional hydrothermal method treatment, organic pollutants such as dioxin in the incineration fly ash can be removed, meanwhile, large-scale continuous treatment is achieved, and the incineration fly ash dioxin treatment process is continuous, safe, convenient, reliable in effect, small in occupied area, economical and efficient.