In order to address the issue of system contamination caused by the treatment of copper ions(Cu2+) wastewater using electrochemical technology, which leads to poor system stability,this paper focused on the pollution characteristics of the system during the removal of Cu2+ by flow electrode capacitive deionization (FCDI), and explored the influence mechanism of key parameters such as applied voltage, inlet Cu2+ concentration, flow electrode velocity, and inlet water quality on the Cu2+ removal performance of the system. The results show that under the conditions of an applied voltage of 0.8 V, an influent Cu2+ concentration of 50 mg/L, and a flowing electrode flow rate of 1.2 mL/min, the Cu2+ removal rate reaches 56.22%, the charge efficiency is 90%, and the copper removal rate is 0.03 μmol/[DK](cm2·min). At the same time, the continuous operation stability of the flow electrode system under different cycling modes is investigated, and the pollution characteristics of the ion exchange membrane and activated carbon electrode are analyzed. The results indicate that the flow electrode exhibits significant advantages in copper ion removal under the single cycle (SC) mode, and the membrane and electrode exhibit the lowest level of pollution. This study provides important reference for the application of FCDI technology in heavy metal removal.