Benthic macroinvertebrate Index of Biological Integrity (B-IBI) was developed of relationships among habitat variables, water quality variables and benthic macroinvertebrate data from 340 sampling sites in the Huntai River for assessment of stream health and standardized reference and impaired sites selection. In this study, 9 reference sites and 6 impaired sites were selected to construct the B-IBI index. Five major benthic macroinvertebrate metric parameters (i.e. taxonomic composition, relative abundance, pollution tolerance characteristics, dominant groups, and functional feeding groups) were assessed by applying the B-IBI. The results showed that the Huntai River is highly degraded and loss of biological integrity in which 24.8% of sampling sites were in "excellent" and "good" conditions, 27.8% of sampling sites were in "normal" conditions, and 47.4% of sampling sites were in "poor" or "very poor" conditions. The box-plot distributions of B-IBI were highly clustered within the references sites, impaired sites and test sites indicated that the assessment was reliable. Moreover, the resulting B-IBI was highly correlated with the data set of macroinverterbates across 70 sampling sites in the Taizi River in May 2009, with 58% of the total sampling sites graded in the same stream health categories and 40.6% of total sampling sites with one grade difference in stream health. This correlation was employed to check the accuracy of the assessment result between standardized sites selection and "expert option" reference sites selection and showed strong consistency between two methods. The regression between the B-IBI and habitat assessment was significant in linear regression (R²=0.25,P<0.01). And the regressions between the B-IBI and conductivity (Cond.), permanganate index (COD_Mn) and ammonia (NH₃-N) were also significant in curved regressions (R²=0.23-0.34,P<0.01). According to the regressions, the inflexion values of three water quality variables were around 1,000 μs/cm (Cond.), 5.0mg/L (COD_Mn) and 1.0mg/L (NH₃-N), respectively. The B-IBI decrease sharply when these water quality variables are lower than the inflexion value and decrease minimally when the concentration is higher than the inflexion value. The COD_Mn and NH₃-N would have significant effect on the stream health and macroinvertebrates communities when the concentration is higher than the III grade of Chinese surface water standards. The sensitivity of the B-IBI and its component metrics to environmental stressors supports the use of this index for monitoring ecological conditions in streams in the Huntai River.