As Chinese economy booms during recent decades, river management attains more investment, and is required to develop more rapidly for flood defense as well as facilitating navigation, which brings a lot of changes and threat to most of aquatics, especially those endangered species. Yangtze finless porpoise is one of those endangered species, of which the habitat is faced up with severe threats from hydraulic engineering. Hechangzhou reach, situating in the lower Yangtze river and 250kmupstream from the Yangtze river estuary(Shanghai), is one of the important navigation channels in Yangtze river and is also one of the main nature re serves for Yangtze finless porpoise. In order to adjust the discharge distribution of the two branches in Hechangzhou reach, Chinese Department of Water Resources conducted a project to construct 2 submerged sills in the north branch of Hechangzhou reach.Acknowledging the importance of both navigation development and protection of endangered Yangtze finless porpoise, investigating the impact of two sub merged sills on the physical habitat of Yangtze finless porpoise is necessary. This requires a good understanding of the hydrodynamics changes caused by two submerged sills as well as the requirements from Yangtze finless porpoise on its physical habitat.  In this thesis, a study is performed to find a reliable evaluating system of Yangtze finless porpoise's physical habitat quality under the impact of hydraulic engineering. Habitat suitability index model, developed by the United States Fish and Wildlife Service (USFWS or FWS),is applied to the physical habitat of Yangtze finless porpoise. By literature reviewing and inquiring biologists, the vital ecological behaviors of Yangtze finless porpoise are identified as movement and feeding, and vital habitat variables are identified as water depth, flow velocity and substrate type.   A previous developed hydro-morphodynamic numerical model was made available and is further developed to gain a better understanding of the changes to local hydrodynamic variables such as water depth, flow velocity. Substrate type, as one of the identified habitat variable from the results of habitat suitability index model, is determined by taking as implified method of comparison between soil critical shear stress and local bed shear stress. Three scenarios are designed to simulate the situation in the dry, normal-water and monsoon season.   This thesis forecasts the changes to the physical habitat quality of Yangtze fineless porpoise through understanding the changes to local hydrodynamic condition and combining the results from habitat suitability index model. Overall,the submerged sills offer limited potential habitat area, slightly extend the high-quality habitat area and improve the existing habitat.