Poyang Lake, located in the middle and lower reaches of the Yangtze River, is the largest freshwater lake in China and the most important habitat for the Yangtze finless porpoise. With the operation of the Three Gorges Dam, the water ecosystem functions of Poyang Lake are deteriorating, which has negatively influenced the habitat of Yangtze finless porpoise. In this research, quantitative functions of the three environmental factors, flow velocity, water depth and food availability, which have the greatest impact on the abundance of Yangtze finless porpoise were constructed, and then a habitat model of the Yangtze finless porpoise was established based on hydrodynamic model. The model results are in good agreement with the observed data, and the simulation well reproduces the spatial position distribution and abundance of the Yangtze finless porpoise in Poyang Lake. Then, the proposed model is applied to compare three scenarios before and after the operation of Three Gorges Dam, and simulate the evolution of hydrodynamics, feeding environment and Yangtze finless porpoise habitat in Poyang Lake. Two typical parts of river-lake connection channel and the main lake area were analyzed separately. Results show that the water depth, surface area and food availability in Poyang Lake are gradually decreasing, which lead to the weakening and plaque-like fragmentation of the Yangtze finless porpoise habitat. The findings in this study could help to understand how changes in aquatic conditions affect the ecological habitat, and provide scientific guidance for the future protection of Yangtze finless porpoise.