Here we report a simple-but-effective method to control the membrane morphology and transport properties of aromatic multi-block copolymers bearing perfluorosulfonic functions, via casting with different counter-cations. Five monovalent cations with different sizes, polarity, hydrophobicity, i.e., H + , Li + , K + , Cs + , TEA + , and one double-valence cation, i.e., Ca 2+ , were selected for manufacturing block copolymer membranes. We show that the counter-cation has a strong impact on the superstructure long-range order by acting as either block-separator, either block-compatibilizer, therefore tuning the thermodynamics of the self-assembly process. Hence, by selecting the cations, highly ordered or completely disordered phase-separated block morphologies can be created. The effect of counter-cation nature on the morphology is strongly reflected on the proton conductivity of acidified membranes. At 25 °C and 10% relative humidity, the acidified TEA +-cast membranes are 22 times less conductive than the acidified Cs +-cast ones. By combining microscopy and neutron scattering techniques, we reveal the direct correlation between enhanced functional properties and quality of membrane microstructure directed by the nature of cations with beneficial characteristics. Our findings highlight the role and importance of cation selection to tailor the functional properties of multiblock ionomers applicable as solid electrolytes for energy conversion devices.