Di- and trifunctional benzimidazole molecules, 1 and 2, have been synthesized as the model compounds to identify their molecular packing structure and hydrogen bond network, which is possibly involved in the proton transfer system belonging to its heteroaromatic functional groups. By carrying out the simple reaction between acid chloride and diamine, the desired benzimidazole model compounds are obtained with high yield above 60%. The comparison studies between the model compounds and benzimidazole reveal that the model compounds show well-packing structure with intermolecular hydrogen bonds similar to those observed in benzimidazole. The presence of solvent with 2 leads to the unique intermolecular hydrogen bonds between one molecule of 2 and six molecules of solvent (i.e., 2-propanol) resulting in the solvent-assisted intramolecular hydrogen bond network among benzimidazole functional groups. The comparative studies of the effect of temperature on the packing structure and hydrogen bond in the model compounds indicate that the development of the benzimidazole unit from monofunctional to difunctional and finally trifunctional enhances the intermolecular interaction between the molecules and results in the stronger molecular packing structure of the compounds. A study on proton conductivity by preparing the sulfonated poly(ether ether ketone) (SPEEK) membranes with benzimidazole, 1, and 2 for 15 phr equivalent to benzimidazole group clarifies (i) incorporation of benzimidazole compounds improves the proton conductivity of SPEEK in dry condition and (ii) the increase in proton conductivity is relevant to the number of benzimidazole group on molecule.