The microstructures of the ionomer–catalyst interfaces in the catalyst layers are important for the fuel cell performance because they determine the distribution of the active triple-phase boundaries. Here, we investigate the ionomer–catalyst interactions in hydroxide exchange membrane fuel cells (HEMFCs) using poly(aryl piperidinium) and compare them with proton exchange membrane fuel cells (PEMFCs). It is found that different catalyst layer microstructures are between the two types of fuel cell. The ionomer/carbon (I/C) ratio does not have a remarkable impact on the HEMFC performance, while it has a strong impact on the PEMFC performance, indicating the weaker interaction between the HEMFC ionomer and catalyst. Molecular dynamics simulations demonstrate that the HEMFC ionomer tends to distribute on the carbon support, unlike the PEMFC ionomer, which heavily covers the Pt nanoparticles. These results suggest that the poisoning effect of the ionomer on the catalyst is much weaker in HEMFCs, and the improved ionomer/catalyst interaction is beneficial for the HEMFC performances.