The partially saturated Vertical Flow Constructed Wetland (VFCW) has been reported to exhibit better nitrogen removal performance than unsaturated VFCW when treating domestic wastewater. However, it is unclear how saturated water level affects the nitrogen transforming and its removal in VFCW. Herein, three VFCWs were operated under 90, 70 and 20 cm saturated water level regime, respectively. The physicochemical parameters of influent and effluent, i.e., chemical oxygen demand (CODCr
), total nitrogen (TN), ammonia (\rmNH^+_4
-N), nitrate (\rmNO^-_3
-N), nitrite (\rmNO^-_2
-N), total phosphorus (TP), as well as the abundance of nitrogen transforming functional genes were investigated. The results showed that the purification performance of VFCW was improved by optimizing the distribution of unsaturated and saturated zones through saturated water level adjustment. The best nitrogen removal performance of 53.6% was obtained when the saturated water level height was 70 cm (media bed depth was 90 cm). The abundance of functional genes suggested that the unsaturated zone had no negative influence on denitrification community. The enriching nitrite oxidation bacteria in the unsaturated zone promoted the simultaneous nitrification and denitrification processes. However, too much low saturated water level (20 cm) might cause the unnecessary loss of carbon sources, resulting in the limited denitrification process and decreasing nitrogen removal efficiency. Hence, the saturated water level regime could be employed to improve the nitrogen removal performance in VFCW.