Highly fluorinated comb-shaped ionomer membranes made by solution casting have shown high proton conductivity coupled with low dimensional swelling upon hydration, which demonstrates their potential as materials for proton exchange membranes (PEM) for fuel cells (FC). Small-angle neutron scattering (SANS) and neutron diffraction studies on the copolymers have been conducted to resolve the morphological structures. Two peaks were found in the SANS curves: the low-q peak is assigned to the strong interaction among the self-aggregating hydrophilic and hydrophobic domains, whereas the high-q peak is attributed to the “ionomer peak”. We propose a new structural model to fit the SANS data in the q range covering 0.005−0.4 Å−1. This model combines a form factor of flexible wormlike aggregates with an ellipsoidal cross section and a structure factor of hard-disk interaction accounting for the low-q scattering as well as the Teubner−Strey model for the high-q “ionomer peak”. Water uptakes can be derived from the best-fitting results of the current model and are consistent with the measured values. The neutron diffraction data indicate that there is little long-range orientation, if any, of the hydrophilic or hydrophobic domains.