This work presents a novel heat-integrated fuel cell stack system with methanol reforming. Its configuration is composed of fuel processing units (FPUs), proton exchange membrane (PEM) fuel cell stack, and heat exchangers (HEXs). Well mixed methanol and oxygen flows in contact with countercurrent flowing water dominates the production of hydrogen at the exit of FPUs and influences the stack temperature. The heat exchange connections can enhance the utilization of energy of FPUs. To ensure the stable steady-state operation, the model-free fuzzy incremental control scheme within the multi-loop feedback control framework is developed. Finally, the proposed system integration and control configuration are verified by closed-loop simulations. Crown Copyright (C) 2009 Published by Elsevier B.V. All rights reserved.