Yangtze River Estuary, the largest estuary of Pacific Coast, is not only the unique channel for the endangered species (Chinese sturgeon) to migrate between Yangtze River and Pacific Ocean ,but also the critical habitat for its juvenile fish to feed and grow. In recent years, human disturbance to the Chinese sturgeon habitat is increasingly serious. The fragmentation、degradation and loss of the habitat are the biggest problems of protecting Chinese sturgeon. Based on several ecological factors statistical study, five habitat characteristics were selected and determined their ranges of the most suitability, and then Suitability Index and Synthetic Index analysis are used to do quantitative evaluation. Suitability Index was verified by the number Chinese sturgeon from tidal nets monitor and water quality and biological data nearby the monitoring station in Chongming Dongtan of the Yangtze River Estuary from the year of 2004 to 2010. At last , the data of the coastal water investigation of Shanghai in summer 2006 were evaluated by two different methods on Geographical Information System(GIS). The study results demonstrated that habitat areas of excellent、good、fair and poor, and habitat suitability index was better than synthetic index method on landscape grain.