We characterized the responses of benthic macroinvertebrates to heavy metals released from mines in high mountain streams of the Gangqu River in the Shangrila Gorge, China. Benthic macroinvertebrates were collected with a kick-net at 32 sampling sites. In addition, 25 environmental variables including heavy metal concentrations were measured at each sampling site. Although the concentrations of heavy metals were not seriously high, their effects were reflected in the changes of community composition of benthic macroinvertebrates. Total abundance and species richness decreased with increasing heavy metal concentrations. Species richness of Plecoptera and Trichoptera, Margalef richness index, and percentage of scrapers in functional feeding groups were negatively correlated with heavy metal concentrations. A high variation was observed in the response of different taxa to heavy metals. Heavy metals mainly affected the sensitive taxa of Plecoptera, Ephemeroptera, and Trichoptera. However, some tolerant taxa were observed in Trichoptera (such as Hydropsyche sp.) and Dugesia sp. Cluster analysis and a non-metric multidimensional scaling analysis were applied to characterize specific macroinvertebrate taxa composition. The analyses revealed the effects of different environmental factors such as geographical, hydromorphological, physical, and chemical factors including heavy metals on the distribution of benthic macroinvertebrates in high mountain streams. Although the effects were compounded with different factors such as altitude, temperature, stream width, turbidity, and heavy metals, the influence of heavy metals on benthic macroinvertebrate communities was clearly identified (decreased species richness, changes in species composition). Even though the contamination of heavy metals was low in the sampling area, the consequences were clear, indicating that long-term exposure to heavy metals could seriously impact aquatic communities in high mountain streams.