Aromatic rings of poly(styrene-b-(ethylene-r-butylene)-b-styrene) triblock copolymer (SEBS) were functionalized with various acid functional groups for proton exchange membrane (PEM) applications. Three different acid functional groups (fluoroalkylsulfonic acid, arylsulfonic acid, and arylphosphonic acid) were introduced into SEBS-via borylation of aromatic C-H bonds and Suzuki coupling reactions. The incorporation of acid side groups selectively into the polystyrene block of SEBS created nanometer-scale phase separated morphology composed of hydrophilic and hydrophobic domains in which the morphology structures and interdomanin distances are dependent on the chemical structure of acid side chains. Despite high ion exchange capacity value, the aryl phosphonated polymer (SEBS-P) showed the lowest water uptake and significantly lower proton conductivity compared to sulfonated SEBS PEMs because of the low acidity of phosphonic acid. Compared to aryl sulfonated SEBS-S-2, fluoroalkyl sulfonated SEBS-S-1 showed better proton conductivity at low relative humidity condition (<50%), which is ascribed to the stronger acidity and more compact ionic domains. Morphology study of SEBS-S-1 indicates that due to both hydrophobic and oleophilic nature of fluoroalkyl chains, fluoroalkyl sulfonate chains of SEBS-S-1 induced more dense ionic self-aggregation.