Based on the data collected from 21 sites in Jian River Basin and historical data, 26 candidate metrics representing attributes of fish assemblage were screened. Of which, tenmetrics passed the initial selection, then the analyses of index value distribution, discrimination ability and Pearson correlation were performed, finally 5 major indicators were used for the biotic integrity index system to assess the environmental quality of Jian River Basin, which are percent of total number of species in expectation, percent of cyprinid species,percent of Acheilognathinae species,percent of tolerant species, percent of species with pelagic eggs. It suggested that the fish-based biological integrity index was good in Ling River, fair in Luo River, poor in Pingding River, Meihua River and the main stream,and Xiaodong River was the worst. As comprehensive health status of rivers was in the worse state, certain measures should be taken for ecological restoration to the relatively healthy state. The assessments were consistent with the actual situation of human disturbance in this river drainage. The established fish biotic integrity index in this study could be used to assess environmental quality or used as reference for rivers in adjacent regions.