A bilayer membrane based on a heterogenous cation exchange membrane with a homogeneous cation exchange layer and a polyaniline on its surface is prepared. The intercalation of polyaniline into the membrane with a homogeneous cation exchange layer is performed by oxidative polymerization of aniline. The influence of the homogeneous cation exchange layer and the polyaniline on the structure, conductivity, diffusion permeability, selectivity, and current–voltage curve of the heterogeneous cation exchange membrane is established. Membrane properties are studied in the HCl, NaCl, and CaCl2 solutions. The homogeneous cation exchange layer has a negligible effect on the transport properties of the initial heterogeneous membrane. The polyaniline synthesis leads to a decrease in the macropore volume in the membrane structure, conductivity, and diffusion permeability. The counterion transport number in the bilayer membrane is significantly reduced in a solution of calcium chloride and practically does not change in sodium chloride and hydrochloric acid. In addition, the asymmetry of the diffusion permeability and shape of current–voltage curve depending on the orientation of the membrane surface to the flux of electrolyte or counterion are found.