A new approach was applied to improve the proton conductivity mechanism in perfluorinated membranes for hydrogen fuel cells. The composite short-side chain membranes were modified with functionalized diamond nanoparticles. Carboxylated nanodiamonds embedded in the polymer matrix provide an increase in conductivity at a moderate nanodiamond content, while the mechanical strength of the membranes remains high. The casting method of membranes preparation from solutions in N,N-dimethylformamide allowed saving the general channel structure in membranes at the presence of nanodiamonds, in agreement with neutron scattering data. We propose the formation of additional areas of conductivity, formed controllably, due to nanodiamond particles associated with polymer chains, on the surface of which accelerated diffusion of protons through the hopping Grotthus mechanism from the centers of proton adsorption proceeds with the transition to proton-conducting channels of the matrix covered with sulfonic groups.