In this paper, we simulate the changes in the structure and transport properties of an anion-exchange membrane (CJMA-7, Hefei Chemjoy Polymer Materials Co. Ltd., China) caused by its modification with a perfluorosulfonated ionomer (PFSI). The modification was made in several stages and included keeping the membrane at a low temperature, applying a PFSI solution on its surface, and, subsequently, drying it at an elevated temperature. We applied 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 µm) 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 exhibits 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 became comparable in its transport characteristics with more expensive IEMs available on the market.