Polybenzimidazole doped with phosphoric acid (PA) is a candidate for polymer electrolyte membranes in fuel cells. Understanding the interaction of benzimidazole in polybenzimidazole with PA is important for fuel-cell applications. Herein, the interaction of a PAbenzimidazole complex was investigated using density functional theory, with calculations performed at the ?B97X-D/6-311G(d,p) level of theory, with an aim to investigate the effects of bibenzimidazole configuration on the interaction energy. Benzimidazole and three different bibenzimidazole configurations (2,2'-bibenzo[d]imidazole (1), 2,5'-bibenzo[d]imidazole (2), and 5,5'-bibenzo[d]imidazole (3)) were used as models for bulk polybenzimidazole. Calculation of various types of hydrogen bond interaction showed that the interaction between the imino moiety of the monomer and the hydroxyl group of PA is the strongest, which agrees with previous studies. Our calculations indicated that pH interactions between the hydrogen atoms of the PA molecule and the benzene rings should be considered, and these contribute to the interaction energy for some interaction complexes. The interaction energy between the monomer and PA is smaller than that of the PA dimer. However, the interaction energy between bibenzimidazole and PA is comparable to that of the PA dimer for bibenzimidazole configurations 1 and 2, highlighting the importance of considering the adjacent monomer unit.