The present invention relates to a control device and a control method of a high voltage inverter capable of automatically and accurately setting up neutral point information at a master controller and a plurality of cell controllers of the high voltage inverter, wherein a master controller determines information of neutral point set up to itself and performs a communication with the cell controllers each disposed at each of a plurality of U phase unit cells, a plurality of V phase unit cells and a plurality of W phase unit cells to determine the neutral point information preset on the cell controllers and to detect a cell controller set up with neutral point information different from that of the master controller, and to correct the neutral point information of the detected relevant cell controller using the neutral point information set up in the master controller, thereby operating the high voltage inverter.