The space gravitational wave detection mission has put forward multiple performance requirements for micro-newton thrusters, such as “fast response, high resolution, and low noise”. In order to solve the problem that the traditional open-loop propulsion system can hardly meet the high-precision performance, the microwave ion thruster with high accuracy and controllability of thrust estimation is adopted as the research object, and the precision feedback control method combining analog circuit and digital control technology is adopted to achieve a resolution of less than 0.1 μN, fast response of 20 ms, and 10−3~1 Hz frequency band noise less than 0.05 μN/Hz1/2 of the thrust performance. Experimental results show that, compared with open-loop regulation, the feedback control can effectively suppress various noises and disturbances caused by device temperature drift and complex operating characteristics of the thruster, and the anti-aliasing filter scheme adopted in this paper can suppress the folding of high-frequency data in the low- and medium-frequency bands during the digital control process, while it can effectively improve the system performance and reduce the impact of thrust noise. The feedback control strategy proposed in this paper verifies the possibility of a microwave ion thruster as an actuator for super “static and precise” space experiment satellites and provides a feasible solution for the application of a microwave ion thruster in deep space science experiment missions such as gravitational wave detection.