Apparatus and method for controlling fuel cell system

An apparatus of controlling a fuel cell system, the apparatus comprising:

• a fuel cell system including a fuel cell stack, a balance of plant (BOP) configured to operate the fuel cell stack, and a fuel cell controller configured to control the BOP;
• a first power converter located between the fuel cell stack and a first voltage battery and including a bidirectional DC/DC converter;
• a second power converter located between the fuel cell stack and a second voltage battery and including a single bidirectional DC/DC converter module;
• and
• a controller configured to operate the first power converter or the single bidirectional DC/DC converter module of the second power converter, when the fuel cell system is started or stopped, and configured to control the first power converter or the single bidirectional DC/DC converter module of the second power converter to supply driving power to the BOP using electrical energy of the first voltage battery or the second voltage battery,
• wherein an output voltage of the second voltage battery is higher than an output voltage of the first voltage battery.