Abstract: As the dominant submerged macrophytes in Poyang Lake, the winter buds of Vallisneria natans provide food for wintering waterbirds. In order to quantify the effects of water level fluctuation on the habitat area of Vallisneria natans in Poyang Lake, a numerical model was developed by integrating an EFDC hydrodynamic model and habitat suitability curves. The habitat of Vallisneria natans in Poyang Lake was continuously simulated since the 175 m impoundment of the Three Gorges Reservoir in 2008. The quantitative response functions between potential habitat area and water level at Xingzi gauge station were developed for two habitat criteria:① suitable habitat based on suitability curves and ② regions with water depth≤4 m where Vallisneria natans can grow. It was found that potential habitat area of Vallisneria natans is maximized when the water level at Xingzi gauge station is around 15 m, producing a suitable habitat area is about 1 703 km² and an area with water depths≤4 m is about 2 336 km². The impacts of Three Gorges Reservoir and proposed Poyang Lake Lock on the potential habitat area of Vallisneria natans were analyzed. The operation of Three Gorges Reservoir could prevent habitat area getting too small, which could guarantee habitat stability. However, the fluctuation of habitat area decreases significantly, with standard deviations of habitat area declining 27% and 47% for potential suitable habitat and regions with water depth≤4 m respectively compared to its pre-operation. For the proposed Poyang Lake lock, in order to decrease its negetive effect on Vallisneria natans habitat, the recommended operation water level during its refill period should be lower than 16 m, and the water level during the refill period of Three Gorges Reservoir should be higher than 13.5 m. This operation results in a reduction in suitable habitat area by less than 20% from the maximum (1 703 km²), and in a reduction in the area of regions with water depth≤4 m less than 10% from the maximum(2 336 km²). The quantitative influence of water level fluctuation on the potential habitat area of Vallisneria natans in Poyang Lake has been clarified, and the quantitative basis for the conservation of Poyang Lake ecosystem under the modified regime of flow and sediment was provided.