This paper proposes a solution to the electromagnetic interference problem caused by large input current harmonics in three-phase power frequency rectifier converters by combining a three-phase EMI filter with a Auto transformer rectifier unit. Through in-depth analysis of the working principle, the relevant parameters are calculated in detail, and the simulation model is built on Simulink. After several parameter iteration designs, the single-phase total input current harmonic is finally reduced to 3.41%. In order to further verify the correctness of the simulation model, a 25 kW engineering prototype is developed. The related load test and CE101 electromagnetic compatibility test were completed. The results show that the single-phase current harmonic distortion rate is about 3.8%. And its short-term overload capacity is strong, which can be loaded to 1.5 times under the condition that the power quality meets the design index. The results fully show that the prototype has excellent performance indicators.