The optimal design of the cathode gas diffusion layer (GDL) for direct methanol fuel cells (DMFCs) is not only to attain better cell performance, but also to achieve better water management for the DMFC system. In this work, the effects of both the PTFE loading in the cathode backing layer (BL) as well as in the micro-porous layer (MPL) and the carbon loading in the MPL on both water transport and cell performance were investigated experimentally. The experimental data showed that with the presence of a hydrophobic MPL in the GDL, the water-crossover flux through the membrane decreased slightly with increasing the PTFE loading in the BL. However, a higher PTFE loading in the BL not only lowered cell performance, but also resulted in an unstable discharging process. It was also found that the PTFE loading in the MPL had little effect on the water-crossover flux, but its effect on cell performance was substantial: the 40-wt% PTFE loading in the MPL was found to be the optimal value to achieve the best performance. The experimental results further showed that increasing the carbon loading in the MPL significantly lowered the water-crossover flux, but a too high carbon loading would decrease the cell performance as the result of the increased oxygen transport resistance; the 2.0-mgCcm−2 carbon loading was found to exhibit the best performance.