Selective separation of monovalent anions with reduced fouling is one of the major challenges for anion exchange membranes (AEM) in electrodialysis (ED). In this research, an alternating current layer-by-layer (AC∼LbL) assembly technology was first proposed and then applied to the construction of a durable multilayer with the selective separation of monovalent anions with reduced fouling. Under an alternating current (AC) electric field, the hydrophilic poly(4-styrenesulfonic acid-co-maleic acid) sodium salt and 2-hydroxypropyltrimethyl ammonium chloride chitosan were homogenized and rapidly assembled on a commercial original AEM and then crosslinked using 1,4-bis(2',3'-epoxypropyl) perfluoro-1-butane. In ED, the permselectivity and the selective separation efficiency [separation parameter between sulfate (SO42-) and chloride (Cl-) ions] of the resulting membrane (AC∼LbL#7.5 AEM) were 4.87 and 62%, respectively, whereas the original AEM had corresponding parameters of 0.81 and -8%, respectively. Furthermore, the AC∼LbL#7.5 AEM still retained a permselectivity of 4.52 and a selective separation efficiency for Cl- of 57% after 96 h of ED operation. In addition, the AC∼LbL#7.5 AEM showed an excellent antifouling property when three types of organic fouling materials: sodium dodecylbenzenesulfonate, bovine serum albumin and humic acid were used as model foulants.