Hydrology and salinity are the most important environmental factors in the salt marsh ecology system, they directly affect the growth and reproduction of wetland plants. In order to better understand the ecological adaptation strategies of saltmarsh plants under the background of salinization of wetlands, and to provide theoretical and technical support for water-salt manipulation and wetland vegetation restoration, the Scirpus nipponicus was selected as the experimental material to study the effects of water levels and salinity on its growth traits and the biomass allocation in Momoge National Nature Reserve. The tested soil was collected in June 2019 from the study area, its salinity was 0.512 ±0.0038 g/L. The S.nipponicus seedlings were cultivated outdoors for 3 weeks before the experiment. We carried out a controlled experiment with six levels of salinity (300, 1000, 2000, 3000, 4000 mg/L and 5000 mg/L) and six water levels(-10, 0, 20, 40, 60 cm and 80 cm). The salinity was controlled by mixing NaCl with NaHCO₃ (molar ratio was 2:1), and the water level was controlled by platforms of different heights. The experiment lasted for 60 days. The individual height and ramet number were determined directly. The biomass of tuber, and the underground, aboveground parts and total biomass were determined after drying to constant weight at 65℃. The biomass allocation indexes included tuber biomass allocation (tuber biomass/total biomass), underground biomass allocation (underground biomass/total biomass), and aboveground biomass allocation (aboveground biomass/total biomass). The results showed that the water level significantly affected individual height (P<0.05), individual height increased first and then decreased with water level increasing. The ramet number was significantly affected by salinity, and it was limited by water level. The ramet number in shallow water increased at the appropriate salinity. The water level, salinity and their interaction significantly affected the biomass accumulation and allocation of S.nipponicus. The biomass of tuber, and the underground, aboveground parts and total biomass all increased first and then decreased with water level and salinity increasing. The total biomass was higher (3.24-3.71 g) at the salinity of 1000-3000 mg/L and the water level of 80 cm. The biomass allocation was significantly affected by water level-salinity interaction. At the salinity of 1000, 2000 mg/L and 3000 mg/L, the tuber biomass allocation and underground biomass allocation increased and the aboveground biomass allocation decreased with the water level increasing. This suggested that S.nipponicus focused on asexual reproduction to adapt to rising water levels. In summary, S.nipponicus grew well at the water level of 40-80 cm and the salinity of 1000-3000 mg/L. The tolerance of S.nipponicus to the water level increased at the appropriate salinity, while the threshold reduced at high salinity.