Highly proton-conductive metal–organic coordination polymers (MOCPs) have attracted a great deal of attention because of their potential applications in proton exchange membrane fuel cells and electrochemical sensors. Currently, the precise control of proton conductivity is mainly achieved through the rational design of organic ligands and the effective modification of pore structures. In contrast, little attention has been paid to the influence of metal ions of MOCPs on their proton conductivities due to the absence of isostructural compounds for comparison and analysis. Herein, we designed three MOCPs {[(H₃O⁺)₂][Zn(pzdc)₂]}_n, {[(H₃O⁺)₂][Mn(pzdc)₂]}_n and [Cu(Hpzdc)₂·2H₂O]_n (H₂pzdc = 2,3-pyrazinedicarboxylic acid) with very similar chemical formulae and single-crystal structures as models to investigate how the coordination interactions/abilities of metal ions affect their proton conductivities and water stabilities. Remarkably, these three MOCPs show proton conductivities as high as 10⁻³ S cm⁻¹ at 323 K and ∼97% RH along with excellent stabilities to temperature, water, acid and base (over a broad pH range of 0–12). Density functional theory (DFT) calculations show that the binding energies of the O–H bonds of the carboxyl groups in the solvation models are a predominant factor in precisely tuning the proton conductivity at ∼97% RH. Furthermore, the extraordinary stabilities, especially in water, are more likely to be associated with the coordination interactions resulting in a significant decrease in the system energies of the generated coordination compounds. These results provide a novel perspective for the design and synthesis of MOCPs with high proton conductivity and good stability.