The multimetric index of biotic integrity (IBI) based on fish assemblages has been widely used to monitor aquatic ecosystem status in headwater streams. However, the application of the IBI has generally been biased by the low number of species and natural altitudinal gradients in these systems. To overcome these limitations, taxonomic distinctness and size-weight-based indices were integrated into our candidate metric pool, and calibration was performed to reduce the effects of the altitudinal gradient on the metrics in our study. Eighty-two sites in six headwater streams along a typical high altitude gradient and with low species richness were sampled. Eighty-three candidate metrics were selected to develop our IBI (IBI-Han) based on the systematic screening method. Six metrics based on taxonomic distinctness, habitat, tolerance guild, reproductive guild and trophic guild were finally retained in the IBI-Han: average taxonomic distinctness, percent rheophilic species, percent tolerant species, percent biomass of water column species, percent lithophilic species, and percent carnivorous species. The IBI-Han performed well in discriminating anthropogenic disturbances not only at training sites but also at testing sites, which suggests that our method could provide a reliable evaluation of the condition of headwater stream ecosystems. Among the six rivers, the Jinshui River showed relatively healthy ecosystem status, while the other five streams were disturbed by various human activities. Our work highlights that taxonomic distinctness indices are robust biomonitoring indices that can be combined with other functional indices to assess high altitude gradient streams in the upper Han River. We believe that the process of developing the IBI-Han could be regarded as a reference for managing headwater streams in other regions of China or in other states.