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Abstract A PEM fuel cell with the Nafion ionomer phase of the cathode catalyst layer (CL) that was exposed to hot dry gas during the hot‐pressing process showed improved performance over the whole current density range and ~ 220% peak power increase with humidified air at 80°C. This enhanced performance is attributed to the modified structure of the perfluorosulfonic acid (PFSA) ionomer layer in the CL during the MEA's hot‐pressing process. The dry gas exposure above the glass transition temperature (T_g) results in the aggregation of the ionic groups to retain the residue water molecules. This process separates the ionomer into ionic‐group‐rich domains and ionic‐group‐sparse domains. The ionic‐group‐sparse domains create hydrophobic interface and reactant transport channels with lower water content and thus higher oxygen solubility in the ionomer. Accordingly, the water‐unsaturated ionomer and its surface hydrophobicity enhance the kinetic‐controlled and concentration‐polarized regions of the fuel cell polarization curve, respectively. The surface hydrophobicity of the ionomer layer is analyzed by the contact angle measurement and XPS. The durability of the hydrophobic effect belowT_gis demonstrated by boiling the treated material. Re‐treating the hydrophobic sample with humidified gas exposure aboveT_geventually exhibits hydrophilic features, further proving the manipulability of the ionic group distribution.