The microstructural modifications associated with the lowering of hydrophilic/hydrophobic phase separation can reduce the molecular permeation in an ionomer without compensating the ionic conductivity significantly. This idea has been investigated by selecting poly (vinyl alcohol) PVA as the polymer matrix of proton exchange membranes. 4-Formyl-1,3-benzenedisulfonic acid disodium salt (DSDSBA) molecules, with two protogenic groups tethered to the rigid aromatic ring are introduced to the polymer chains as ion carriers. With a view to improve the morphological stability, glutaraldehyde is used as the crosslinking agent. The molecular chemistry such as flexible backbone, short and rigid side chains and dense acid functionalities improved the selective proton conduction through the membranes. The ionomers show up to eight times selectivity as that of Nafion for protons over methanol. The XRD, DSC and FTIR results are employed to establish the microstructural features of hydrated membranes. Large sorption of nonfreezing water is identified as the main reason for the attractive DMFC membrane characteristics of the prepared membranes. A detailed analysis of the state of water in the prepared membranes reveals that well connected system of narrow water channels allowed for low methanol permeation along with high mobility of protonic charge carriers.