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Three phase three level neutral point clamped (NPC) rectifier is a popular topology for power converter front-ends to achieve controllable DC voltage. In this paper, its mathematical model is analyzed and a dual-loop control strategy is adopted to regulate both DC voltage and input power factor. Instead of space vector PWM, an improved multi-level carrier based PWM is presented. The control system is developed on DSP and a FPGA is employed to generate the PWM signals. The effectiveness of the proposed scheme is verified by the experimental results.