A two-dimensional two-phase mass transport model for liquid-feed direct methanol fuel cells (DMFCs) is presented in this paper. The fluid flow and mass transport across the membrane electrode assembly (MEA) is formulated based on the classical multiphase flow theory in the porous media. The modeling of mass transport in the catalyst layers (CLs) and membrane is given more attentions. The effect of the two-dimensional migration of protons in the electrolyte phase on the liquid flow behavior is considered. Water and methanol crossovers through the membrane are implicitly calculated in the governing equations of momentum and methanol concentration. A modified agglomerate model is developed to characterize the microstructure of the CLs. A self-written computer code is used to solve the inherently coupled differential governing equations. Then this model is applied to investigate the mechanisms of species transport and the distributions of the species concentrations, overpotential and the electrochemical reaction rates in CLs. The effects of radius and overlapping angle of agglomerates on cell performance are also explored in this work.