The drive architecture with many power converters in parallel is typically used in distributed electric propulsion systems, which are a key avenue in the development of electrification for all-electric aircraft, electric ships, and other transport vehicles. With the increase of the number of converters, electromagnetic interference will be intensified, which directly threatens the safe and stable operation of the system. In order to suppress the conducted interference generated by parallel drive systems, a modulated wave phase-shifting control strategy is proposed. Based on the in-depth analysis of the coupling mechanism of electromagnetic interference noise in the system, the conducted interference equivalent model of the parallel drive system is established through the cascade of a multi-port network model. By introducing real-time position current compensation, the modulation wave of each driver is controlled by phase-shifting, so that the common mode noise generated by each driver cancels out each other. The simulation and experimental verification are carried out in a MATLAB/Simulink simulation environment and a darkroom experiment environment for a dual-motor parallel drive architecture. The results show that when the phase difference of the driver modulation wave is 360°/m(m is the number of parallel drivers), the noise reduction is most significant. This technique greatly lowers the system's conducted interference without appreciably altering the system performance index, and it works well with parallel drive systems that have the same drive module specifications. It has a certain reference value for the design of a distributed electric drive system.