Polybenzimidazoles (PBIs) are the most promising binders for the catalyst layer (CL) in high‐temperature proton exchange membrane fuel cells (HT‐PEMFC). However, traditional commercial PBIs are not applied in binders because they do not enhance the electrochemical performance and because the related solvents are not environmentally friendly. In addition, proton transfer channels in PBIs are not investigated at the microscopic and atomic scales to date. In this study, a nitrogen‐rich rigid PBI binder containing pyridine, diazofluorene, and partially grafted nitrile (PBPBI‐3CN) is prepared with a functionalized structure, good thermal stability, and good solubility in an environmentally friendly solvent. A membrane electrode assembly (MEA) is fabricated with the PBPBI‐3CN binder, providing a high peak power density, low resistance, and good stability. The protonation, hydrogen bond networks, and platform for proton transfer are confirmed in the CLs. The protonation of PBPBI‐3CN occurs in two steps. First, some phosphoric acid (PA) molecules bind to nitrogen‐containing acidophilic groups via preliminary protonation; second, multiple PA molecules then interact with nitrogen‐containing acidophilic groups via further protonation. With protonation as the foundation, a sufficient amount of PA molecules form a hydrogen bond network, and proton transfer channels are established. As nitrogen‐rich binders for high‐temperature proton exchange membrane fuel cells (HT‐PEMFCs), PBPBI‐3CNs have good solubility in environmentally friendly solvents and high thermal stability; they provide HT‐PEMFCs with promising electrochemical performance. Modeling via experiments and simulations shows the importance to nitrogen‐containing acidophilic interaction positions and provides a theoretical foundation for the establishment of proton transfer channels in the two‐step protonation mechanism.