A new design concept for ion-conducting polymers in anion exchange membranes (AEMs) fuel cells is proposed based on structural studies and conformational analysis of polymers and their effect on the properties of AEMs. Thermally, chemically, and mechanically stable terphenyl-based polymers with pendant quaternary ammonium alkyl groups were synthesized to investigate the effect of varying the arrangement of the polymer backbone and cation-tethered alkyl chains. The results demonstrate that the microstructure and morphology of these polymeric membranes significantly influence ion conductivity and fuel cell performance. The results of this study provide new insights that will guide the molecular design of polymer electrolyte materials to improve fuel cell performance.