A typical working mode for the fuel cell hybrid system is that the fuel cell produces constant power output while the auxiliary storage energy device such as ultracapacitor or battery provides the deviation between the desired power demand and the value of the actual operation. This paper concentrates on the control of the fuel cell flow system. The system which is like an under-actuated mechanical system needs to control two objects (the cathode pressure and the air flow) with one manipulated variable (the set voltage of the air mass flow controller). A SIRMs-based fuzzy inference model is successfully implemented in the system. Online random search optimization algorithm based on Simulink C-S functions is developed to adjust the parameters in the model. By alternative control of the two objects, experimental results demonstrate the realization of the control strategy with one adjustment means. Copyright (C) 2013, Hydrogen Energy Publications, LLC. Published by Elsevier Ltd. All rights reserved.