Drag free control system, as a key part of space gravitational waves detection satellite, needs to offset non-conservative forces on the satellite and reduce its residual acceleration. As the actuator of drag-free control system, the micro propulsion system needs to output super low-noise thrust to realize the detection goal. The microwave discharge ion thruster (MDIT) and microwave discharge cusped field thruster (MDCFT) are two minimized electric thrusters designed by Harbin Institute of Technology (HIT), which both can realize 1-100μN thrust range. However, high thrust noises in the low frequency band limit their applications on the space GWs detection task. Analyses of thrust noise sources show the main disturbances are ionization processes. Based on it, a feedback control system is designed according to the characteristics of the two thrusters. Then an experimental platform is established on ground to validate that the thrust noises of MDIT and MDCFT both can be reduced below 0.1μN/Hz1/2 in 1mHz to 1Hz after adopting the feedback control system.