Disclosed herein is an apparatus for controlling a fuel cell system, which includes multiple hot boxes including multiple fuel cell stacks, using a reconfigurable network having linear switching complexity, includes: a power conversion system for supplying outputs of normal stacks among the multiple fuel cell stacks to a load; at least one auxiliary power conversion system for supplying an output of at least one deteriorated stack among the multiple stacks to a load; a reconfigurable switch network for connecting in series or in parallel stacks of any hot box to stacks of another hot box; and a control unit for controlling an operation of the reconfigurable switch network by detecting a state of each of the stacks.