We investigate two types of polysulfone-based membranes (quaternary ammonium-functionalized anion exchange membrane and sulfonated proton exchange membrane) using molecular dynamics simulations to compare their nanophase-segregated structures and transport properties. Although the distribution of ionic groups on the polymer backbone is similar for both types, the quaternary ammonium groups and hydroxide ions in the anion exchange membrane are more solvated by water compared to the sulfonate groups and hydronium ions in the proton exchange membrane. Correspondingly, such better solvation of the ammonium groups and hydroxide ions leads the internal structure to a less matured hydrogen bonding network in the water phase, especially at low water content conditions. Through analysis of the nanophase segregation of the membranes, it is found that the characteristic correlation length has a similar value for both membranes, whereas the concentration contrast between the polymer domain and water phase is more distinct in the anion exchange membrane relative to the proton exchange membrane. Within such nanophase-segregated structures, it is found that the diffusion of hydroxide is ∼6% and ∼11% of that of hydronium at 10 and 20 wt % of water content, respectively, which might be due to the strong correlation at ∼4 Å among the hydroxide in the anion exchange membrane.