Methods for synthesizing hybrid MF-4SC membranes containing silica whose surface has been modified with proton acceptor amine-containing groups (3-aminopropyl- and 3-(2-imidazoline-1-yl)-propyl-) are proposed. The incorporation of surface-modified silica particles into the membrane matrix leads to a decrease in the water uptake and exchange capacity compared to a membrane containing pure SiO2. The proton conductivity and diffusion permeability of NaCl and HCl solutions and the H+/Na+ ion interdiffusion are studied. The proton conductivity of the membranes containing surface-modified silica is higher than that of the parent membrane and the membrane containing pure SiO2. It is shown that the surface modification of silica with 5 mol % of nitrogen-containing groups results in a decrease in the diffusion permeability and an improvement in the ion transport selectivity. This extraordinary change in the properties is caused by an increase in the size of the pores and the channels that connect them, along with a significant decrease in the free volume within the pores. At the same time, an increase in the amount of modifying groups to 10 mol % leads to a sharp acceleration of the diffusion permeability and interdiffusion processes because of the formation of through pores in the membrane matrix.