The present invention provides a power configuration system for a fuel cell hybrid vehicle and a method for controlling the same, in which a second blocking diode is installed in a main bus terminal at an output terminal of a fuel cell (in front of a first blocking diode) separately from the existing first blocking diode installed in the main bus terminal, the positions of high voltage components for driving the fuel cell are changed from the rear of the first blocking diode to the front of the first blocking diode, and the operations of the high voltage components are appropriately controlled during regenerative braking such that the voltage of the fuel cell may be maintained below that of the supercapacitor.