A procedure for the fabrication of profiled cation-exchange bilayer membranes with the homogenized surface based on the commercial membrane MK-40 has been developed. The surface morphology and membrane microstructure have been studied by atomic-force microscopy, electron microscopy, and standard contact porosimetry. The concentration dependences of the electrical conductivity and diffusion permeability of the profiled and bilayer profiled membranes have been studied. It has been shown that the application of an MF-4SK film on the surface of the profiled membrane results in a decrease in its diffusion permeability and some increase in specific conductivity. Based on the data obtained, the transport and structure parameters have been calculated in terms of the microheterogeneous model to assess the influence of the modification on the properties of the support membrane. The current-voltage characteristics of the membranes have been measured in sodium chloride solutions, and it has been shown that profiling leads to an increase in the limiting current by 40%. The investigation of mass transfer of ions in the channels formed by the support and modified membranes has shown that under intense current regimes, the mass transfer coefficient through the profiled bilayer membrane is one and a half times that through the initial profiled membrane.