Intermolecular and intramolecular hydrogen bond (H-bond) and proton transport in acid-base complexes and amphoteric molecules consisting of phosphonic acid groups and nitrogenous heterocyclic rings are investigated by density functional theory calculations and H-1 NMR and P-31 NMR spectroscopy. It is concluded that a phosphonic acid group can act both as H-bond donor and H-bond acceptor, while an imine nitrogen atom can only act as H-bond acceptor and an amine group as H-bond donor. And the intramolecular H-bond is weaker than the intermolecular H-bond attributing to configurational restriction. In addition, the strongest H-bond interaction is observed between a phosphonic acid and a 1H-indazole because of the formation of double H-bonds. The H-1 NMR and P-31 NMR chemical shifts for the acid-base complexes are consistent with the density functional theory calculations. From the H-1 NMR chemical shifts, fast proton exchange is observed between a phosphonic acid and 1H-benzimidazole or 1H-indazole. Finally, it is proposed that polymeric material tethered with 1H-benzimidazole or 1H-indazole rings is a favorable component for high-temperature proton exchange membranes based on acid-base complexes or acid-base amphoteric molecules.