We report herein temperature- and humidity-controlled small-angle X-ray scattering (SAXS) analyses of proton-conductive ionomer membranes. The morphological changes of perfluorosulfonic acid polymers (Nafion and Aquivion) and sulfonated aromatic block copolymers (SPE-bl-1 and SPK-bl-1) were investigated and compared under conditions relevant to fuel cell operation. For the perfluorinated ionomer membranes, water molecules were preferentially incorporated into ionic clusters, resulting in phase separation and formation of ion channels. In contrast, for the aromatic ionomer membranes, wetting led to randomization of the ionic clusters. The results describe the differences in the proton-conducting behavior between the fluorinated and nonfluorinated ionomer membranes, and their dependence on the humidity.