The acidic amphiphilic compound H[Co(H2L1)(HL1)(phen)]·3H2O (H4(Co-L1), H3L1 = 5-(3', 5'-dicarboxylphenyl)-pyridine-2-carboxylic, phen = phenanthroline) and the hydrophilic compound [Ni(HL2)(H2O)5]·H2O (H(Ni-L2), H3L2 = 5-(3',5'-dicarboxylphenyl)-pyridine-3-carboxylic) were synthesized via hydrothermal reactions at acidic conditions. The acidity of H4(Co-L1) is stronger than of H(Ni-L2); while the hydrogen bond continuity in H4(Co-L1) extended monodirectionally, which is smaller compared to the three-directional extension observed in H(Ni-L2). The proton conduction behaviors of these two compounds as fillers of Nafion composite membranes have been investigated. The results indicate that the optimal doping amounts of H4(Co-L1) and H(Ni-L2) are 2 and 1%, respectively; the proton conductivities of H4(Co-L1)/Nafion-2 and H(Ni-L2)/Nafion-1 composite membranes are 0.243 and 0.212 S·cm-1, respectively, which are approximately 50.2 and 30.6% higher than that of pure Nafion membrane, respectively. A higher doping amount of H4(Co-L1) can be attributed to its hydrophobic phen ligand, which promotes compatibility with Nafion membrane and reduces aggregation. Hydrogen bond continuity has a more significant effect on proton conductivity than acidity at relatively low doping amounts; conversely, this relationship reverses at relatively high doping amounts.