The present work shows a strategy to apply hydrogen bond connected benzimidazole compounds for improvement of proton conductivity and thermal stability of sulfonated poly(ether ether ketone) (SPEEK). A series of benzimidazole derivatives, i.e., mono-, di- and trifunctional benzimidazole, are applied to study the role of their packing structures related to the specific properties for SPEEK in being a proton exchange membrane. The benzimidazole-based compounds significantly increase the thermal stability of the SPEEK and, at the same time, improve proton conductivity of SPEEK under anhydrous condition at temperatures higher than 80 °C. The investigation of the structural effect of the benzimidazole based model compounds implies that the trifunctional benzimidazole molecule is the most effective compound to improve the thermal stability and the proton conductivity of SPEEK as compared to mono- and difunctional ones.