A proton conducting hydrated membrane on the basis of sulfonated aromatic poly(ether-ether-ketone) was modeled for the first time using dynamic density functional theory (the “mesoscopic dynamics” method). The model constructed was used to demonstrate the microphase separation of hydrophilic and hydrophobic polymer chain units in the selected region of parameters. A spatial network of water domains formed in the membrane volume. The domain walls consisted of polar (sulfonated) macromolecule units. A comparison with the well-studied Nafion-1100 membrane showed that the cross sections of water channels in the two systems had similar values. This must ensure approximately equal ionic conductivity characteristics.