High-power three-level voltage-source converters are widely utilized in high-performance AC drive systems. In several ultra-power instances, the harmonics on the grid side should be reduced through multiple rectifications. A combined harmonic elimination method that includes a dual primary-side series-connected winding transformer and selective harmonic elimination pulse-width modulation is proposed to eliminate low-order current harmonics on the primary and secondary sides of transformers. Through an analysis of the harmonic influence caused by dead time and DC magnetic bias, a synthetic compensation control strategy is presented to minimize the grid-side harmonics in the dual primary side series-connected winding transformer application. Both simulation and experimental results demonstrate that the proposed control strategy can significantly reduce the converter input current harmonics and eliminates the DC magnetic bias in the transformer.