In order to probe the effects of polymer microstructure on the properties of proton conducting polymer membranes, three series of fluorous−ionic graft copolymers, partially sulfonated poly([vinylidene difluoride-co-chlorotrifluoroethylene]-g-styrene) [P(VDF-co-CTFE)-g-SPS], comprising controlled graft lengths and degrees of sulfonation were synthesized. The parent building block was a poly(vinylidene difluoride-co-chlorotrifluoroethylene) [P(VDF-co-CTFE)] macroinitiator (Mn = 3.12 × 105 g/mol) synthesized to contain 1 chloro group per 17 repeat units, onto which polystyrene, having degrees of polymerization of 35, 88, and 154 units per graft, was grown by atom transfer radical polymerization (ATRP). These graft copolymers, termed short, medium, and long graft chains, were sulfonated to different extents to provide a series of polymers with varying ion exchange capacity (IEC). The resulting P(VDF-co-CTFE)-g-SPS copolymers were cast into proton exchange membranes, and their nanostructure, morphology, and properties were studied. TEM revealed that all three membrane series exhibit a disordered phase-separated morphology comprised of small interconnected ionic clusters varying from 2 to 4 nm in size. For a given IEC, membranes prepared from the short graft chain series possessed larger ionic domains due to their relatively higher degree of sulfonation (DS), which facilitates ion clustering. For short graft membranes, water contents and conductivities were less influenced by IEC. For high IEC membranes, ∼2.50 mmol/g, the short grafts remained water-insoluble, absorbed less water, and afforded higher conductivity than longer graft analogues. These results demonstrate the importance of polymer microstructure on the morphology of membranes, the size of ionic clusters and their ionic purity, and the microstructure’s role in water sorption and proton conductivity. From a technological viewpoint, it indicates that short ionic graft polymers enhance the elastic forces in the matrix and inhibit excessive swelling, allowing high IEC vinylic polymers to remain insoluble. As such, these architectures warrant further investigation as they reduce swelling and promote proton transport under reduced lambda values.