Abstract: Considering low-frequency disturbance of thrust caused by unexpected electrical breakdown and temperature drift in the operation of microwave ion thruster, as well as the ultra-low bandwidth and strong robustness requirements of the drag-free system, which is converted into a frequency domain constraint index, a fractional-order PID was designed as a drag-free controller with perturbation suppression capability as objective function. Simulation study shows that the control had good robustness to various disturbances of the system compared with the classical PID controller, and could suppress the control effects brought by thruster firing and temperature drift, and finally achieved higher control accuracy. The research provides reference for the high-precision control method of gravitational wave detection without dragging satellite considering micro-propulsion system.