Hybridization of inorganic pillars and proton exchange membrane have been studied for increasing performance of proton exchange membrane fuel cell such as working under low relative humidity. For developing hybrid membrane, understanding of morphological structure is crucial. In this study, we synthesize silica mesostructured cellular foam (Si-MSU-F) and meso-structured aluminosilicate with hexagonal network (Al-MCM-41) and study morphological evolution of the membrane by using atomic force microscopy. When Nafion is composited with Si-MSU-F and Al-MCM-41, the hybrid membrane surface is evolved to different structure compare with the pristine Nafion. In addition, Si-MSUF/Nafion shows different morphological structure as Al-MCM-41/Nafion hybrid membranes due to different hybridization mechanism between pillars and Nafion.