Small-angle neutron scattering has been used to study the structure of dry and wet perfluorinated short side chain membranes first synthesized by a new aqueous emulsion method. These membranes are new prospective materials for hydrogen fuel cells and have advantages over long side chain Nafion-type membranes. Experiments enabled us to recognize the subtle features of the membrane structure being responsible for the proton conductivity. The parameters of pores interconnected and forming the channels for diffusion of water molecules and protons were determined as dependent on the chemical composition of the membranes. It was discovered that there was an influence of molecular weight and equivalent weight, varied during synthesis, on the polymer structure.