Ion-exchange membranes (IEMs) are widely used in desalination, waste water treatment, food, energy production and other applications. There is a strong demand for cost-effective IEMs characterized by high selective transport of ions of a certain sign of charge. In this paper, we simulate the experimental results of V. Sarapulova et al. (IJMS 2021) on the modification of an inexpensive anion-exchange membrane (CJMA-7, Hefei Chemjoy Polymer Materials Co. Ltd., China) with a perfluorosulfonated ionomer (PFSI). The modification was made in several stages including keeping the membrane at a low temperature, applying a PFSI solution on its surface, and subsequent drying it at an elevated temperature. We apply the known microheterogeneous model with some new amendments to simulate each stage of the membrane modification. It has been shown that the PFSI film formed on the membrane-substrate does not affect significantly its properties due to the small thickness of the film (4 m) and similar properties of the film and substrate. The main effect is caused by the fact that PFSI material “clogs” the macropores of the CJMA-7 membrane, thereby blocking the transport of coions through the membrane. In this case, the membrane microporous gel phase, which has a high selectivity to counterions, remains the primary pathway for both counterions and coions. Due to the above modification of the CJMA-7 membrane, the coion (Na+) transport number in the membrane equilibrated with 1 M NaCl solution decreased from 0.11 to 0.03. Thus, the modified membrane becomes comparable in its transport characteristics with more expensive IEMs available on the market.