A control system includes first and second fundamental control units for generating first and second fundamental commands, and a compensation control unit. The compensation control unit includes first and second calculation elements and a comparator for comparing first and second modulation indexes. When the first modulation index is less than the second modulation index, the first calculation element generates a first source-side compensation command. When the first source-side compensation command is not sufficient to balance the neutral point voltage, the first calculation element further generates a first line-side compensating command. When the first modulation index is greater than the second modulation index, the second calculation element generates a second line-side compensation command. When the second line-side compensation command is not sufficient to balance the neutral point voltage, the second calculation element further generates a second source-side compensating command.