A fuel cell generation system control apparatus performs a method for controlling power of a fuel cell generation system. A monitoring device monitors power of the one or more fuel cell modules. A controller compensates for power of one or more first fuel cell modules by one or more second fuel cell modules, based on the monitored power, and performs power control of the one or more fuel cell modules. The fuel cell generation system control apparatus addresses a problem in which power of the fuel cell generation system is reduced as there is a change in external environment or an increase in driving time upon power control of a multi-module fuel cell system.