In order to reduce the conducted electromagnetic interference in the auxiliary power supply of the airborne stationary converter, and to improve the realism of the simulation when the auxiliary power supply is subjected to electromagnetic interference, an EMC model of the auxiliary power supply based on the joint simulation of pspice and simulink is built. The model combines the advantages of simulink in the design and implementation of control strategies and the advantages of pspice in the accurate simulation of electronic components, which can directly and easily verify the EMC scheme at the design stage, and on this basis, an effective method of noise suppression combining control strategies and traditional EMI filters is proposed. From the principle analysis to get the accurate model to the conclusion of the joint simulation, it has practical guidance for the auxiliary power supply EMC design and the solution of noise interference problem.