Flow electrode capacitive deionization (FCDI) has great advantages in high salinity wastewater desalination. However, due to the limited adsorption capacity of electrode material, membrane concentration polarization would form and increase energy consumption, and affect the continuity of desalination. In this work, milling technology was used to modify original activated carbon (AC), the obtained ball milled activated carbon (BAC) was used as FCDI electrode material. The milling process modified multiple physical and electrochemical characteristics of original AC. The highest average salt removal rate (ASRR) of BAC was 2.2 times of that of AC, which was attributed to the modified surface properties including more oxygenated functional group, larger electrostatic gravitation characteristics and better hydrophilicity. The reduced concentration polarization during the desalination was responsible for the increased adsorption capacity, which was due to larger electrolyte contact area, enhanced ions capacity by more suitable pore structures, and 5 times higher energy normalized removal salt (ENRS) of BAC flow electrode than that of AC. Because of its simple operation and remarkable modification effect, ball milling technology shows great potential in large scale modification of electrode materials.