Abstract The performance of high temperature proton exchange membrane fuel cell (HT-PEMFC) is significantly affected by the carbon monoxide (CO) in hydrogen fuel, and the flow channel design may influence the CO poisoning characteristics by changing the reactant flow. In this study, three-dimensional non-isothermal simulations are carried out to investigate the comprehensive flow channel design and CO poisoning effects on the performance of HT-PEMFCs. The numerical results show that when pure hydrogen is supplied, the interdigitated design produces the highest power output, the power output with serpentine design is higher than the two parallel designs, and the parallel-Z and parallel-U designs have similar power outputs. The performance degradation caused by CO poisoning is the least significant with parallel flow channel design, but the most significant with serpentine and interdigitated designs because the cross flow through the electrode is stronger. At low cell voltages (high current densities), the highest power outputs are with interdigitated and parallel flow channel designs at low and high CO fractions in the supplied hydrogen, respectively. The general distributions of absorbed hydrogen and CO coverage fractions in anode catalyst layer (CL) are similar for the different flow channel designs. The hydrogen coverage fraction is higher under the channel than under the land, and is also higher on the gas diffusion layer (GDL) side than on the membrane side; and the CO coverage distribution is opposite to the hydrogen coverage distribution.