The aim of the study is to improve the performance of thin-film composite (TFC) membranes with a thin selective layer based on chitosan (CS) via different approaches by: (1) varying the concentration of the CS solution; (2) changing the porosity of substrates from polyacrylonitrile (PAN); (3) deposition of the additional ultrathin layers on the surface of the selective CS layer using interfacial polymerization and layer-by-layer assembly. The developed membranes were characterized by different methods of analyses (SEM and AFM, IR spectroscopy, measuring of water contact angles and porosity). The transport characteristics of the developed TFC membranes were studied in pervaporation separation of isopropanol/water mixtures. It was found that the application of the most porous PAN-4 substrate with combination of formation of an additional polyamide selective layer by interfacial polymerization on the surface of a dense selective CS layer with the subsequent layer-by-layer deposition of five bilayers of poly (sodium 4-styrenesulfonate)/CS polyelectrolyte pair led to the significant improvement of permeance and high selectivity for the entire concentration feed range. Thus, for TFC membrane on the PAN-4 substrate the optimal transport characteristics in pervaporation dehydration of isopropanol (12–90 wt.% water) were achieved: 0.22–1.30 kg/(m2h), 99.9 wt.% water in the permeate.