This paper aims to analyze the membrane electrode assembly (MEA) of the direct methanol fuel cell (DMFC) in order to provide a reference for the design of DMFC. The slow kinetics of methanol oxidation and whether the anode should be hydrophobic or hydrophilic were seldom discussed in previous research. Therefore, this paper focuses on the electrode of the anode. The anodic gas diffusion layer (GDL) is treated with different hydrophilic degrees. Then, the microstructure of GDL is examined using SEM. The water content and water droplet contact angle of GDL were measured. The results are then compared with each other to determine the optimal treatment procedure of the anode. The second part of this paper proposed a new design of the DMFC system. After choosing the appropriate MEAs for the DMFC stack, the stack was combined with the water circulatory system, air circulatory system, and electricity controller to complete the DMFC system. The efficiency of the whole system is discussed.