To improve the fuel efficiency and total exergetic efficiency of a non-isothermal direct methanol fuel cell (DMFC) system, the multi-objective optimization problem is addressed in this article. Under incommensurable multiple goals, the fuzzy inference with two-phase procedures is applied for finding the locally Pareto-optimal solution. Through an iterative optimization programming, a piecewise optimal control action is effectively generated at each time period. Finally, the optimal operating manner by manipulating anode inlet temperature is successfully demonstrated by the dynamic simulation. (C) 2010 Professor T. Nejat Veziroglu. Published by Elsevier Ltd. All rights reserved.