The selective separation of ions in aqueous solutions is of significant importance for water purification and resource recovery. Capacitive deionization (CDI) has emerged as a novel electro-driven desalination process that is gradually being applied in the selective separation of target ions from multicomponent solutions. By utilizing customizable electrode materials, interfaces, and adaptable operating conditions, CDI offers substantial advantages in modulating ion adsorption processes, thereby achieving selective separation of target species. This review provides a retrospective analysis of the developmental trajectory of CDI, with a focus on the mechanisms employed for the selective removal of ions from water using innovative electrode and membrane materials. Additionally, we delve into discussions on the impact of material chemical modifications and various operational factors on CDI selectivity. The paper also highlights several challenges faced by CDI in practical selective separation applications, including the limited selectivity potential of traditional carbon-based electrodes, the need for the development of novel membrane materials, incomplete evaluation systems for selective separation performance, and inadequate research in system design. Furthermore, this review provides insights into the future prospects of CDI in industries such as electronics, rare earths, and food, providing guidance to researchers for the development of low-carbon and efficient CDI selective separation processes.