The microstructure of polymer electrolyte membranes plays a key role in ion conductivity and water transport. Herein, fluorinated poly(aryl ether)s with tetra-alkylsulfonate side chains (SFPAEs) have been successfully synthesized from the copolymerization of a newly developed tetra-allyl-containing bisphenol (TABP) monomer, followed by the thiol-ene addition with sodium 3-mercapto-1-propanesulfonate to attach the ionic groups at the end of the flexible chains. Being the first of its kind, the densely distributed and lengthy alkylsulfonate group possesses the benefit of ease to self-assemble into hydrophilic domains during membrane preparation via solution casting. Indeed, the TEM characterizations revealed that distinct hydrophilic channels of ∼1 − 2 nm width had been formed, much larger than those of a home-made control sample where only di-alkylsulfonate side chains were attached. The SFPAE-4-45 with an IECw of 2.0 mmol g − 1 exhibited an enhanced proton conductivity of 143.7 mS cm−1 at room temperature, which was superior to that of Nafion 212 (91.0 mS cm−1). Furthermore, the oxidative stabilities of SFPAEs were significantly higher than those of non-fluorinated analogs in literature. This study offered a new route to engineering the pendent structure of ionomers for well-defined microscopic morphologies.