Ion back-difusion hinders the practical application of conventional fow-electrode capacitive deionization (FCDI) under long-term operational conditions. To address this challenge, the present study integrated cation intercalation deionization (CID) with FCDI. A novel PFCDI-CID system was developed by utilizing a modifed Prussian blue analogues owing to their enhanced rheological and electrochemical properties. The PFCDI-CID system achieved a high charge efciency of 89.77% and an energy-normalized removal salt of 0.69 mol kJ⁻¹ in single-cycle (SC) mode with the fow electrodes mass fraction of 2% and a desalinized water chamber-to-concentrated saline water chamber ratio of 2:1. Furthermore, under continuous operation for 12 h in SC mode, the PFCDI-CID system maintained stable desalination performance within the frst 2 h. Over an extended duration, the average charge efciency of the PFCDI-CID system was maintained at 88.44%, with an average energy-normalized removal salt of 0.65 mol kJ⁻¹. The mechanism revealed that the desalination process involving the Prussian blue analogues primarily involves Na⁺ intercalation, accompanied by a small amount of electro-sorption process. This system exhibits the characteristics of conventional FCDI while enabling desalination and concentration of simulated saline water during brine discharge, thereby mitigating the impact of ion back-difusion and broadening the application scope of FCDI.