Current fuel cell proton exchange membranes (PEM) rely on a random network of conducting hydrophilic domains to transport protons across the membrane. Despite extensive investigation, details of the structure of the hydrophilic domains in these membranes remain unresolved. In this study a dynamic self-consistent mean field theory has been applied to obtain the morphologies of hydrated Perfluorosulfonic Acid (PFSA) (equivalent weight of 1100) as a model for Nafion® at several water contents. A coarse-grained mesoscale model was developed by dividing the system into three components: backbone, side chain, and water. The interaction parameters for this model were generated using classical molecular dynamics. The simulated morphology shows phase separated micelles filled with water, surrounded by side chains containing sulfonic groups, and embedded in the fluorocarbon matrix. For λ<6 (λ gives the ratio of water molecules to sulfonic groups), the isolated domains obtained from simulation are nearly spherical with a domain size smaller than that fitted to experimental SANS data. For λ>8; the domains deform into elliptical and barbell shapes as they merge. The simulated morphology, hydrophilic domain size and shape are generally consistent with some experimental observations.