Abstract The cathode catalyst layer (CL) in direct methanol fuel cells (DMFCs) has been optimized through a balance of ionomer and porosity distributions, both playing important roles in affecting proton conduction and oxygen transport through a thick CL of DMFC. The effects of fabrication procedure, ionomer content, and Pt distribution on the microstructure and performance of a cathode CL under low air flowrate are investigated. Electrochemical methods, including electrochemical impedance, cyclic votammetry and polarization curves, are used in conjunction with surface morphology characterization to correlate electrochemical characteristics with CL microstructure. CLs in the form of catalyst-coated membrane (CCM) have higher cell open circuit voltages (OCVs) and higher limiting current density; while catalyzed-diffusion-media (CDM) CLs display better performance in the moderate current density region. The CL with a composite structure, consisting both CCM and CDM, shows better performance in both kinetic and mass-transport limitation region, due to a suitable ionomer distribution across the CL. This composite cathode is further evaluated in a full DMFC and the cathode performance loss due to methanol crossover is discussed.