The Taihu lake basin span across Jiangsu，Zhejiang，Shanghai，it is one of the most densely populated，well developed in agricultural and industrial production，GDP and per capita income of the fastest growing regions in China. After the outbreak of Taihu lake water crisis，in the end of may，2007，joint efforts were taken to Taihu governance and it achieved initial results.，the safety of drinking water were effectively ensured and the water environmental quality was improved. The government just concern about water quality index for a long time，but ignored the aquatic ecosystem health and biodiversity protection. East Tiaoxi River is one of important rivers into the Taihu Lake，intensified human activities in recent years resulting in river basin water environment deterioration，Taihu lake fish diversity declination and community structure simplification. in this paper，River health of East Tiaoxi River Basin was as the research object，on the foundation of fish and fish habitat types diversity research and their relation with environmental stress factors，index evaluation method based on fish biological integrity index （F - IBI） was presented，and through the field investigation，selection and assignment，a suitable evaluation index system of the region was established. Through practical application on river basin scale，the index system has proved that it can be used as a common tool in different types of river ecosystem health evaluation of Taihu lake basin.