Faradaic deionization (FDI) has been proposed as an effective solution to the desalination. However, developing a cathode material that possesses high desalination efficiency, lower energy consumption and good stability remains a significant challenge. Herein, we prepared urchin-like AlV3O9 (AlVO) microsphere with different crystal structure using hydrothermal process followed calcination as cathode material for capacitive deionization. Among them, lamellar AlVO-350 with interlayer crystalline waters of the hydroxide group exhibit a desalination capacity of 92.97 mg g−1 and notably a better cycling stability due to the synergistic effect of coordinated water charge shielding and hydrogen bonds stabilities on layered structure. On the other hand, the AlVO-550,which has a higher ratio of V5+/V4+, provided a desalination capacity of 101.70 mg g−1. It achieves a charging efficiency of 88.6% and an energy consumption of 0.329 kWh kg−1, which attributed to the high proportion of V5+ in VO slabs, facilitating Na+ intercalated reactions. This work opens up pavement for designing more advanced electrode materials for FDI.