Disclosed herein is an apparatus for controlling a fuel cell system, including: a plurality of stack state detecting units for detecting respective states of a plurality of fuel cell stacks; a switching unit for connecting at least parts of the plurality of fuel cell stacks to each other in series or in parallel; and a control unit for detecting at least one degraded stack based on the states of the stacks detected by the plurality of stack state detecting units, and forming at least one degraded stack unit including the detected at least one degraded stack by controlling the operation of the switching unit, so the apparatus can quickly and easily connect the stacks to each other in series, in parallel or in series-parallel using cheap electric switches instead of using a plurality of power conditioning system (PCS).