The embodiment of the application provides a control system and a control method for a fuel cell. According to the control system and the control method, operation states of all monitoring points of afuel cell stack can be acquired and comprise a directly-acquired state indicator and an indirect reckoning indicator based on a monitoring value; furthermore, controlled quantity can be solved by using a fuzzy control mode according to operating state indicators and preset deviation; integrated control over electrical output performance of the fuel cell, the humidity of a proton exchange membraneand the stack temperature can be realized; the control system and the control method adapt to the characteristics of multiple input parameters and uncertain nonlinear time variation, and the advantages of comprehensive control factors and quick deviation response are achieved.