To explore the community status, the spatial distribution pattern, and the relation to environmental factors, a detailed investigation of macroinvertebrates in Danjiangkou Reservoir was carried out in the autumn (November) of 2013. In this study, a total of 35 species were identified, thereinto, Limnodrilus hoffmeisteri and Branchiura sowerbyi were the common species, while Limnodrilus hoffmeisteri and Tubifex tubifex were the dominant. The macroinvertebrates had significant spatial differences in community, and their standing crops were at a high level, without obvious decline. In terms of the status of macroinvertebrate community (ⅡCS, the integral index of the community state), the Hanjiang region was better than the Danjiang region, and the Kuxia was better than the Kuzhong and Kuwan. The co-inertia analysis (CIA) and canonical correspondence analysis (CCA) were applied to reveal the environmental preferences of the main species and the important environmental factors that affecting the species spatial distribution. The results of CCA analysis showed that water temperature, turbidity, conductivity, dissolved oxygen, chlorophyll a, antimony, total nitrogen, molybdenum, permanganate index, and boron had significant effects on species distribution. The results of partial least-square (PLS) showed that pH, conductivity, total nitrogen, boron, molybdenum, antimony, barium, and vanadium could well predict the ⅡCS, being the limiting factors for the community development. Combining CCA with PLS, conductivity, total nitrogen, boron, molybdenum and antimony were the main environmental factors with important effects on macroinvertebrate communities.