In order to understand the aquatic organism resources and characteristics of aquatic ecological environment after ecological water transportation in the lower reaches of the Tarim River basin， from 2019 to 2020， the community structure of macroinvertebrates in the middle and lower reaches of Tarim River， Qarqan River and Taitema Lake were investigated， and the environmental influencing factors were evaluated. The survey results showed that a total of 97 taxa of macroinvertebrates taxa， belonging to 3 phyla， 4 classes， 10 orders and 27 families， were identified in this study. Aquatic insects were the main groups （82 species）， among which Diptera （47 species）， Coleoptera （14 species） and Odonata （13 species） were the most numerous taxa. Chironomidae species were dominant in different regions. The average density and biomass of benthic animals peaked in May， which were much higher than those in August and October， but the diversity indices had no significant difference among different time and space （P>0.05）. The main functional feeding groups in Tarim River and Qarqan River were collector gatherers （95.89%， 91.86%）， while the main functional feeding groups in Taitma Lake were collector gatherers （50.68%） and predators （34.12%）. The Mantel correlation analysis showed that ammonia nitrogen， dissolved oxygen and potassium permanganate were the main environmental factors affecting the diversity and functional groups of benthic animals. The results showed that the composition of the macroinvertebrates community in the Tarim River basinwas relatively simple and the ecological environment was relatively fragile. Therefore， it is necessary to carry out and deepen the ecological restoration and management of the rivers in this area.