While flow-electrode capacitive deionization (FCDI) is recognized as an attractive desalination technology, its practical implementation has been hindered by the ease of scaling and energy-intensive nature of the single-cell FCDI system, particularly when treating brackish water with elevated levels of naturally coexisting SO 4 2− and Ca 2+ . To overcome these obstacles, we propose and design an innovative ion-selective metathesis FCDI (ISM-FCDI) system, consisting of a two-stage tailored cell design. Results indicate that the specific energy consumption per unit volume of water for the ISM-FCDI is lower (by up to ∼50%) than that of a conventional single-stage FCDI due to the parallel circuit structure of the ISM-FCDI. Additionally, the ISM-FCDI benefits from a conspicuous disparity in the selective removal of ions at each stage. The separate storage of Ca 2+ and SO 4 2− by the metathesis process in the ISM-FCDI (46.25% Ca 2+ , 14.25% SO 4 2− in electrode 1 and 4.75% Ca 2+ , 35.25% SO 4 2− in electrode 2) can effectively prevent scaling. Furthermore, configuration-performance analysis on the ion-selective migration suggests that the properties of the ion exchange membrane, rather than the carbon species, govern the selectivity of ion removal. This work introduces system-level enhancements aimed at enhancing energy conservation and scaling prevention, providing critical optimization of the FCDI for brackish water softening.