Micro motors are widely used in daily life equipment and industrial drive systems. Various countries have proposed corresponding electromagnetic compatibility standards for electronic equipment. The conducted interference and radiated interference of a micro motor system exported to Europe exceed the EN55032 standard. According to the control principle and structure of the motor, it is re-designed to improve the conducted interference and radiated interference under the condition of fixed installation size. The electromagnetic interference source and propagation path of the controller are theoretically analyzed. The components of common mode current and differential mode current are classified by Fourier transform. The interference source is weakened by adjusting the driving resistance and switching frequency and adding the RC absorption circuit, and the propagation of electromagnetic interference is suppressed through ground filtering, so that the electromagnetic interference is reduced. Experimental results show that adding filter circuit can reduce conducted interference, and adding RC absorption circuit can reduce radiated interference.