We report results of multiscale simulations of a hydrated ionomer membrane based on sulfonated poly(ether ether ketone) (sPEEK) that constitutes an important class of the promising membrane materials for fuel cell applications. Using atomistic and field-theoretic simulation techniques - classical molecular dynamics and dynamic density functional theory - we study the processes of self-organization in sPEEK membranes in the presence of water. At the same water content, both simulation techniques predict a similar structure of the hydrated membranes. The observed membrane morphology can be represented as a topologically complex sponge-like network consisting of irregular water-filled channels. Compared to Nafion, the channels in the sPEEK membrane are narrower. Nevertheless, the estimated percolation threshold in sPEEK is lower than for Nafion.