The invention relates to an mN stage thrust-continuously-adjustable electric propulsion system and method based on an HEMPT thruster. The system comprises the HEMPT thruster, an electric propulsion control unit, a proportional flow storage and supply unit and a digitization adjustment power unit; the electric propulsion control unit is controlled under on-star control commands to generate two drive control signals, the first drive control signal is sent to the proportional flow storage and supply unit, and the second drive control signal is sent to the digitization adjustment power unit; meanwhile, the electric propulsion control unit collects a first telemetry signal fed back by the proportional flow storage and supply unit and a second telemetry signal fed back by the digitization adjustment power unit, and a telemetry package is formed to be sent to an external on-star computer; and the thruster generates mN stage thrust-continuously-adjustable thrust. The system has the beneficial effects of being simple, reliable, small in weight, low in working voltage, wide in thrust adjusting scope and the like. By means of the design of the system, continuous adjustment of the thrust can be achieved, the thrust adjusting scope reaches 1 mN to 20 mN, and the thrust resolution ratio is superior to 15 muN.