Abstract Since the construction of the Gezhouba Dam in the 1980s, the number of Chinese sturgeon in the Yangtze River has been rapidly declining. The Gezhouba Dam has cutoff the migration path of these sturgeon, resulting in an overall reduction of suitable sturgeon habitat. This paper describes a habitat suitability index model that is used to evaluate the impacts of the Gezhouba Dam and Three Gorges Project on Chinese sturgeon spawning sites. Based on research concerning the reproduction characteristics of Chinese sturgeon, ten major ecological factors that influence reproduction were analyzed, including: water temperature, velocity, water depth, substrate, suspended sediment concentration, and the amount of egg predatory fish. The suitability index (SI) curves based on these ten ecological factors were obtained, and a habitat suitability function was developed. A two-dimensional mathematical model was also created to simulate and predict physical habitat situation (such as hydraulic, sediment, and substrate) of the Chinese sturgeon. By coupling the habitat suitability function and a two-dimensional mathematical model, a habitat suitability index model for Chinese sturgeon was established. The habitat suitability index model was validated by comparing measured data with predictions from the model. These comparisons showed that the computed results agreed well with the measured results, and the high calculated habitat suitability index (HSI) corresponded to high measured quantity of eggs per unit (1000 m3) discharge (CPUEd). The calculated habitat suitability index for Chinese sturgeon also showed that the habitat suitability index was better in 1999, before the impoundment of the Three Gorges Project, compared with the habitat suitability in 2003. Simulation results of different discharges from Gezhouba Dam predicted that flow discharges between 10,000 and 30,000 m3/s were most suitable for sturgeon spawning.