Aiming at on-line controlling of Direct Methanol Fuel Cell (DMFC) stack, an adaptive neural fuzzy inference technology is adopted in the modeling and control of DMFC temperature system. In the modeling process, an Adaptive Neural Fuzzy Inference System (ANFIS) identification model of DMFC stack temperature is developed based on the input-output sampled data, which can avoid the internal complexity of DMFC stack. In the controlling process, with the network model trained well as the reference model of the DMFC control system, a novel fuzzy genetic algorithm is used to regulate the parameters and fuzzy rules of a neural fuzzy controller. In the simulation, compared with the nonlinear Proportional Integral Derivative (PID) and traditional fuzzy algorithm, the improved neural fuzzy controller designed in this paper gets better performance, as demonstrated by the simulation results.