Abstract Electrode structure determines the rate of transport and electrochemical reactions and is significantly affected by the catalyst deposition method. In this study, the effect of catalyst deposition is investigated on the pore structure, mass transport, and operating performance of the catalyzed electrodes prepared by the methods of catalyst coated on membrane (CCM) and catalyst coated on substrate (CCS). The result indicates that the CCS electrode is thinner, yielding larger porosity, smaller geometric pore surface area, smaller diffusion and permeation resistivity, and lower cell performance. The maximum power density of the CCS electrodes is only about 4% smaller than that of the CCM electrodes at high Pt loadings (0.4 mg·cm−2), while it is as much as 60% less than that of the CCM counterparts at low Pt loadings (0.1 mg·cm−2). The significant performance drop for the low-Pt-loading CCS electrodes is due to the relatively low surface area in the catalyst layers resulted from catalyst penetration into the pores of the gas diffusion layer, even though the mass transfer resistivity is smaller than their CCM counterparts. The CCS method is therefore unsuitable for low-Pt-loading electrodes (