A numerical model is developed to predict the performance of a microchannel methanol steam reformer with different catalyst layer configurations to produce hydrogen-rich syngas for a high temperature polymer electrolyte membrane fuel cell (HT-PEMFC). A solution schema is developed to compare continuous catalyst layer configurations and various segmented catalyst layer configurations without any convergence issue in numerical analysis. In this work, heat is provided to the endothermic reforming-side via methanol combustion. The results show that higher heat transfer rates can be provided by applying segmented catalyst layer configurations thus, resulting in significant performance improvement of the microchannel methanol steam reformer. The results reveal that methanol conversion can be increased by similar to 25% by using segmented catalyst layer configurations with less catalyst in the reforming and combustion sides. The results also indicate that even though there is no significant improvement in methanol conversion with increasing catalyst layer thickness, the greater catalyst layer thickness provides the advantage of reduced high temperature elevations across the reformer length. Overall, the segmented catalyst layer configurations can play an important role in designing a next generation of microchannel reformers for fuel cell power generation systems to maximize power, minimize reformer size, and decrease the required quantity of the catalyst.