In ion exchange membrane processes (e.g. electrodialysis), improving ion selectivity and reducing water permeance are two key concerns, which drive new membrane fabrication methods. Preparation of composite ion exchange membrane with functional layers may be a solution to elevate its performance. In this study, composite anion exchange membranes (C-AEM) were prepared by using layer-by-layer (LbL) method, and were characterized with regard to membrane surface properties, selectivity, as well as water permeance. Results indicate that monovalent ion selectivity increased with the number of assembled layers. More specifically, when the membrane was modified with 10.5 layers, P-SO4(2-) (Cl-) reached over 10, which was much higher than the commercially available monovalent selective membrane (ACS, P-SO4(2-) (Cl-) around 5). Besides, the C-AEMs also showed a good performance on organic ion selectivity and water migration control. This work proves that LbL method is an effective way to prepare functionalized ion exchange membrane by controlling membrane surface properties (surface potential and pore size). Furthermore, this work provides an investigation of transport mechanisms of ions with different charge, different size and different hydration number by penetrating functional membranes with layered top structure. The prepared C-AEMs showed a good separation efficiency of monovalent ions and organic acids with controlled water migration, this may be potentially used in desalination, wastewater treatment, chemical separation, or other related fields.