Abstract Proton conductors with engineered charge‐assisted hydrogen‐bonding networks are pivotal for advancing proton exchange membrane fuel cells (PEMFCs). Herein, a novel proton‐conducting supramolecular clusters, ([Bi 6 O 5 (OH) 3 ] 2.24 [PW 12 O 40 ] 1 [NO 3 ] 2.4 [H 3 O] 5.8 , BPN) has been synthesized and characterized. Molecular dynamics (MD) simulations reveal that charge‐assisted dynamic O─H⋯O hydrogen bonds mediate the supramolecular assembly, while water molecules facilitate proton transport pathways. The material exhibits a maximum proton conductivity of 0.12 S cm −1 at 90 °C and 97% (RH) relative humidity, which is comparable to that of Nafion. The spin‐lattice relaxation time ( T 1 ) of the Bi–O adsorbed protons is significantly shorter than that of the W‐O adsorbed protons, indicating that the protons at the Bi–O sites have a higher migration rate. 1 H magic‐angle spinning NMR ( 1 H MAS NMR) and density functional theory (DFT) calculations reveal [Bi 6 O 8 ] enhances proton mobility, while [PW 12 O 40 ] stabilizes transition states, lowering the activation barrier to 0.14 eV. The BPN‐Nafion hybrid membrane enhances direct methanol fuel cell performance with an open‐circuit voltage of 0.82 V and power density of 86 mW cm −2 . This integrative design strategy—synergizing inorganic cluster units with dynamic hydrogen‐bonding networks—establishes a scalable platform for developing PEMFC materials with programmable proton transport pathways and improved operational stability.