A control system includes a fundamental control unit, first and second compensation control units, a switch control unit, and a switch implementation unit. The fundamental control unit generates fundamental commands to implement fundamental power conversion operation for a converter. The first compensation control unit generates a first compensation signal for injection into the fundamental command to balance neutral point voltage when the converter is in operation in a first state. The second compensation control unit generates a second compensation signal for injection into the fundamental command to balance neutral point voltage when the converter is in operation in a second state. The switch control unit detects first and second states of the converter and provides first and second switch signals respectively. The switch implementation unit switches the fundamental control unit to communicate with the first and second compensation control units according to the first and second switch signals respectively.