A new class of fully hydrophilic multiblock copolymers consisting of pendant sulfoalkoxyl side chains and hydrophobic oligo(phenylene ether ketone)s have been prepared as proton exchange membranes for fuel cells. The high density of sulfonic acid groups together with the side chain flexibility greatly enhanced the phase separation as well as the proton conductivities of the membranes. In particular, a membrane with a low ion exchange capacity (IEC) of 1.41 mequiv. g⁻¹ showed better ion conduction capacity than Nafion (NRE 212) over the entire relative humidity (RH) range (30–95%). Furthermore, it also exhibited outstanding PEM fuel cell performance at 70 °C under various RH conditions, i.e., higher power densities of 0.768, 0.626 and 0.410 W cm⁻² were achieved at 80%, 50% and 30% RH, respectively, compared to those of Nafion. By calculating the Flory–Huggins χ-parameters, a mesodynamics simulation approach from coarse-grained (CG) modeling was carried out to capture the qualitative morphologies. The modeling results were consistent with the observations from transmission electron microscopy (TEM) images and provided insightful structure–performance relationships. Overall, the results of this work suggest that these types of copolymers have tremendous potential as alternatives to perfluorosulfonic acid membranes in PEM fuel cell applications.