Acid‐functionalized polymers enhance the performance of phosphoric‐acid‐doped polybenzimidazoles (PA/PBIs); however, studies on examining the mechanisms driving these enhancements are scarce. Furthermore, the nanophase morphology of PA‐dependent proton‐exchange membranes has been rarely explored, despite its direct role in the distribution of PA and protonic conduction. In this study, theoretical and experimental analyses to evaluate the microphase separation, particularly the formation and in situ transformation of a two‐phase interface, in a defect‐free polyphenylene ionomer (SPP‐QP) with excellent integrity are performed. SPP‐QP serves as a fortifying agent with an enhanced microphase‐separation ability within PA/PBI‐based membranes. Specifically, the distinct swelling behavior of PA results in the formation of PA‐rich and PA‐poor regions. Thus, the formation of a durable interface that is impervious to PA degradation between SPP‐QP and PBI is critical for facilitating microphase separation. A single cell composed of the composite membrane offers a peak power density of 719 mW cm−2 at 160 °C. Moreover, the durability of a single cell is much longer than 150 h. The results obtained in this study provide insights into the micromorphology and membrane properties observed in the presence of PA.