The heat transfer model of a micro Direct Methanol Fuel Cell (μDMFC) based on heat transfer mechanisms is presented. Three kinds of patterns of the heater integrated into a μDMFC are designed and simulated using the Finite Element Analysis (FEA). The simulation results illustrate that the different patterns of the heater cause different temperature distributions on the surface of the plate,which would induce different heating effects on a fuel cell and great influence on its performance. According to the results,an ideal heater resistance which causes a maximum temperature contrasts of 1.4℃ is applied to control the operating temperature in experiments,for it shows an improvement on the temperature uniformity.Moreover,the heaters with other two patterns produce the maximum temperature contrast of 2.1℃ and 3.0℃,respectively. Experimental results show that the μDMFC can generate a maximum power density of 5.55 mW/cm² at a temperature of 58.2℃ when a current of 53.9 mA is applied to the heater. This work would make it possible for a μDMFC to enhance the performance by adjusting to the temperature and to employ it in extreme environments.