A fine 2D hydrodynamic model of Lake Poyang was used to simulate the hydrological effect of the bathymetry changes between 1998 and 2010. Spatio temporal patterns of water levels and discharge in 2006 of two DEM were simulated to assess the bathymetry effect, considering 2006 as a typical dry year. Results showed that the north water way was deeper in 2010 than that in 1998, resulting in lower water levels. In low water level period, the water surface gradient was larger, and the effect of DEM changes was more significant than that in high level period.The low water levels decreased by 1-2 m corresponding to water level lower than 9 m at Hukou. The reductions of high water levels were lower than 0.4 m when water level at Hukou higher than 15 m. The influenced magnitude was largest at Duchang, followed by Xingzi, Tangyin and Kangshan.The water head from Duchang to Hukou decreased by 2 m in low level period. The water surface gradient decreased from Duchang to Xingzi, and increased from Tangyin to Duchang. There was no distinct gradient change from Kangshan to Hukou. The total discharge into the Yangtze River increased by 6%. The channel areas were most affected, however the influence of bathymetry changes spread across the most of the lake area.Water areas of some sub-lakes varied due to the local morphological changes. This study quantified magnitude and domain of the effect of bathymetry changes on Lake Poyang level from a hydrodynamic perspective. The outcomes may provide scientific support for water resource and ecological environment management, evolution and analysis of river-lake relationship.