The invention provides a control system and a control method of an FPGA soft-core processor technique-based satellite-borne microwave radiometer. The control system comprises an FPGA chip, a communication chip, a level switching circuit, a data acquisition board interface and an antenna driving interface slot, wherein the FPGA chip is matched with the communication chip, the level switching circuit and a data acquisition board to realize the system control of the satellite-borne microwave radiometer and finish the system functions, such as data acquisition, remote measurement, RAD control, antenna control and bus communication, of the microwave radiometer. The control system adopts the FPGA chip to realize a control circuit of the satellite-borne microwave radiometer and increase the integration of the control circuit, and the formed system has a small volume and low power consumption, is suitable for data processing with a higher speed requirement, and has high reliability. Besides, because the programmability of an FPGA is high, only a program inside the FPGA is changed to ensure that the FPGA can be suitable for the control system of the microwave radiometer with different requirements.