Common-mode voltage (CMV) can greatly reduce the reliability and performance of back-to-back two-level converter-fed motor drive systems. To address this issue, a novel CMV elimination scheme based on reference voltage decomposition is proposed in this article. Firstly, the reference voltage of each phase is decomposed into two virtual reference voltages, resulting in six virtual reference voltages that are inter-related for back-to-back two-level converters. Then, by comparing each virtual reference voltage with a triangle carrier based on the two-level pulse width modulation (PWM), the final PWM voltage of each phase can be obtained from the differences of the corresponding two virtual PWM outputs. With the proposed method, both the amplitude and RMS value of CMV can be eliminated theoretically with satisfactory output waveform qualities. Simulations and experimental results are presented to verify the proposed method.