The direct methanol fuel cell is one of the most promising candidates for the next generation power source of small electric appliances. One of the issues, however, is that carbon dioxide bubbles in the anode channel tend to obstruct the reaction and deteriorate the overall fuel cell performance. In this paper, intensive studies were carried out regarding the influence of thickness and wettability of the gas diffusion layer (GDL) on the output voltage and the bubble behavior. The two-phase flow was visualized using a single cell visualization setup with pressure sensors. The results showed that the GDL thickness did not have a strong influence on the fuel cell performance, but the difference in wettability of GDL surface had a distinguished impact on the output voltage and the channel pressure fluctuation.