Designing novel polymer architectures is a key to maintain high proton conductivity for proton-conducting membranes (PCMs) while reducing fuel permeability at a medium water content. Modifying anion exchange membranes with alkyl side-chains is a common strategy to improve the aforementioned membrane properties. This improvement is attributed to the flexibility and dynamics of alkyl side-chains, which speed up the hand-to-hand process of anion diffusion. In this study, we employed this strategy for PCMs and propose hypothetical model membranes to improve proton conduction. To this end, a series of model sulfonated poly(ether sulfone) block copolymers with sulfonate groups attached to the backbone with 0, 6, 10, and 16 carbon unit spacers have been made. Then, we analyzed the morphological properties of the membranes and dynamical properties of water, hydronium ions (H 3 O + ), and methanol by using molecular dynamics simulations. We find that the morphological parameters of the PCM and the hydrophilic domains are almost robust against alkyl side-chain lengths. Nevertheless, the diffusion coefficients of water and hydronium ions increase with a side-chain length of up to 10 carbon units (around 50%) and decrease for membranes with a spacer length of 16 carbons at λ = 15. Moreover, the methanol diffusion coefficient increase, despite the substantial improvement in sulfonate group mobility, remains marginal (below 15%) with a spacer length; hence, a considerably better membrane selectivity is achieved. The results put forward a new design strategy and produce a general understanding of the structure−function interplay for the new generation of PCMs.