Abstract Effect of degree of sulfonation on dynamic mechanical properties, dehydration rate, crystallinity, thermal stability and other fuel cell properties ( e.g. proton conductivity, ion exchange capacity, water uptake capacity, etc. ) of SPEEK membrane are studied and correlated with microstructure. With increasing degree of sulfonation (DS), α-relaxation peak shifts from 135 to 166 °C, while β-relaxation changes from 76 to 37 °C. This peak attribution indicates a plasticizing effect of SO 3 H group within the crystalline region. Thermal stability of SPEEK decreases while peak degradation temperature for desulfonation and glass transition temperature increase from 320-340 and 191–210 °C, respectively with increasing DS from ∼72 to ∼128%. Likewise, small angle X-ray scattering peak at scattering vector of 0.2 A −1 shifts to 0.28 A −1 with an associated increase in intensity due to the evolution of microstructure. Increase in number of scattering centers with progressive sulfonation leads to ionic aggregation, which is the main responsible factor for such evolution. Ionic aggregation is further confirmed by the occurrence of two closely spaced melting peaks in the range of 322–328 and 361–365 °C in differential scanning calorimetry analysis. Dehydration rate gradually increases with increasing DS. Ion exchange capacity, proton conductivity, water uptake and dehydration rate increase from ∼0.49 to ∼2.43 mmol g −1 , ∼1.07 × 10 −4 to ∼2.9 × 10 −2 Scm −1 , ∼20.36 to ∼135.3% and ∼0.296 to ∼0.51 sec −1 , respectively with increase in DS from ∼72 to ∼128%. Microstructure become more homogeneous (less phase separated) at DS of ∼128% resulting in continuous ionic channels for proton conduction.