The aging effects of sodium hydroxide (NaOH) on ion-exchange membranes were systematically studied, including the membrane properties, desalination performance, and fouling behaviors. After aging in NaOH solution, there were minor changes in the cation-exchange membrane (CEM) properties; however, functional groups (i.e., quaternary amines) on the anion-exchange membranes (AEMs) were converted into benzylic alcohol, alkene, and tertiary amines, respectively, by nucleophilic substitution, Hofmann elimination, and ylide formation. These degradations rendered decreased ionexchange capacity (IEC), increased electrical resistance, lost hydrophilicity, and weakened mechanical strength. Moreover, severe deteriorations of desalination performance were observed due to the little ion-exchange ability of the degraded AEMs. The desalination rates were restored after cultivating the aged AEMs in acid solution, mainly because the tertiary amines transformed from the hydroxide form (OH-form) to the ionic chlorine form (Cl-form). The restored desalination rates indicated that the main degradation products were tertiary amines. In addition, the antifouling performance decreased in the order of aged OH-form > aged Cl-form > original AEMs due to the reduction of foulant−membrane intermolecular interactions after aging in NaOH solution. The results contribute to establishing a more comprehensive understanding of the effects of alkaline cleaning on IEMs and provide new insights into cleaning-process optimization and membrane modification.