The purpose of this study was to analyze the composition, and spatial and temporal distribution of the functional feeding groups of large benthic animals in the Lijiang River, as well as their responses to changes in riverine habitat based on four sampling surveys of three study areas in the upper, middle, and lower reaches of the Lijiang River, from September 2009 to August 2012. The results showed that scrapers were the main component in the Lijiang River community, followed by filter-collectors gather-collectors, predators, and shredders. The dominant scraper species were Cipangopaludina cathayensis and Semisulcospira amurensis. The dominant filter-collector species were Corbicula fluminea and Hydropsyche. The dominant gather-collector species were Ephemerellidae and Chironomidae larvae. The dominant predator species were Glossiphonia complanata and Dragonfly nymphs, and the dominant shredder species was Helichus sp. The evaluation of the Lijiang River ecosystem based on the metrics of functional feeding groups showed that the effect of human activities on the stability of habitat was greater than that of tourism. Environmental factors, such as dissolved oxygen, pH, electrical conductivity, temperature, turbidity, chemical oxygen demand, and total nitrogen, were strongly correlated with the functional feeding groups of macroinvertebrates in the Lijiang River.