Proton-conducting superacidic polymer membranes with different fluoroalkyl sulfonate pendants attached to aromatic polymer backbones were synthesized via C-H functionalization and Suzuki coupling reactions. Variation in the chemical structures of the pendant acidic sulfonate moieties and their effects on membrane properties including water uptake, ion exchange capacity, morphology, and proton conductivity were systemically investigated. Membranes containing the short -OCF2SO3H pendant (PSU-S-5) showed a smaller hydrophilic domain size and lower proton conductivity than those containing the longer pendants -OCF2CF2SO3H (PSU-S-1) and -SCF2CF2SO3H (PSU-S-4), likely due to the short chain's less favorable aggregation and lower acidity. Polymer electrolyte membranes with unique branched fluoroalkyl sulfonate pendants (PSU-S-6) gave larger ionic domain sizes, more uniform hydrophilic channels, and higher proton conductivity than samples with analogous linear pendant chains (PSU-S-1), indicating that branched sulfonate structures may be a key future direction in the field of fuel cell membrane.