The selective separation of metal species from various sources is highly desirable in applications such as hydrometallurgy, water treatment, and energy production but also challenging. Monovalent cation exchange membranes (CEMs) show a great potential to selectively separate one metal ion over others of the same or different valences from various effluents in electrodialysis. Selectivity among metal cations is influenced by both the inherent properties of membranes and the design and operating conditions of the electrodialysis process. The research progress and recent advances in membrane development and the implication of the electrodialysis systems on counter-ion selectivity are extensively reviewed in this work, focusing on both structure–property relationships of CEM materials and influences of process conditions and mass transport characteristics of target ions. Key membrane properties, such as charge density, water uptake, and polymer morphology, and strategies for enhancing ion selectivity are discussed. The implications of the boundary layer at the membrane surface are elucidated, where differences in the mass transport of ions at interfaces can be exploited to manipulate the transport ratio of competing counter-ions. Based on the progress, possible future R&D directions are also proposed.