Constructing the ordered catalyst layer is one of the most effective strategies to maximize the catalyst utilization in direct methanol fuel cells (DMFCs). To gain insight into the mass and charge transports in ordered catalyst layer, herein, a two-dimensional two-phase mass-transport model involving Knudsen diffusion was proposed. It is found that the simulation results of the model with Knudsen diffusion are more consistent with the experimental results than that of the model without Knudsen diffusion. It has been demonstrated that higher porosity near the oxygen diffusion layer facilitates the oxygen transport, and the optimal porosity is obtained by balancing mass and charge transport resistances in the ordered catalyst layer. In contrast, higher catalyst loading near membrane improves the cell performance significantly. The highest peak power density of 56.5 mW/cm2 is achieved, when the catalyst loading of the outer and inner layer is 0.15 mg/cm2 and 0.85 mg/cm2, respectively.