The temperature models of anode and cathode of direct methanol fuel cell (DMFC) stack were established by using radial basis function (RBF) neural networks identification technique to deal with the modeling and control problem of DMFC stack. An adaptive fuzzy neural networks temperature controller was designed based on the identification models established, and parameters of the controller were regulated by novel back propagation (BP) algorithm. Simulation results show that the RBF neural networks identification modeling method is correct, effective and the models established have good accuracy. Moreover, performance of the adaptive fuzzy neural networks temperature controller designed is superior.