Irtysh River in Xinjiang Uygur Autonomous Region is the only river in China that disgorges into Arctic Ocean and tremendously abundant in natural resources of zoobenthos throughout the drainage basin. In the present study, we conducted an investigation on the community structure of macrozoobenthos in Irtysh River in July, August and October 2012 and May 2013, which focused on the mainstream, five main tributaries and one affiliated reservoir. We identified 117 macrozoobenthos species, of which 106 species were aquatic insects (90.6%), 6 species were Mollusca (5.1%), 3 species were Oligochaetas (2.6%) and 2 species belonged to other macroinvertebretes (1.7%). The dominant species were composed primarily of Cinygmula sp., Baetis sp., Orthocladius sp., Ephemeridae sp., Polypedilum sp., Apedilum sp., Limnodrilus hoffmeisteri, Cheumatopsyche sp., Ephemerella sp., and Diamesa sp. The density (P=0.558) and biomass (P=0.464) of macrozoobenthos showed no significant seasonal difference. The average density and biomass of macrozoobenthos were 519.05 ind·m^-2 and 3.30 g·m^-2, respectively. The density showed a significant spatial difference, with a higher mean value in the upstream (604.53 ind·m^-2) than in the downstream (447.82 ind·m^-2). Annual mean values of Margalef, Shannon, Simpson and Pielou’s indices were 1.12, 0.53, 0.65 and 0.52, respectively. Clustering analysis was applied for assessing the diversity status of macrozoobenthos at different sampling sites of Irtysh River. The results showed that the community structure of macrozoobenthos was divided into two types: (i) one group had low diversity index at sampling sites 1, 6, 8 and 9; (ii) the other group exhibited relatively high diversity at other sampling sites. Based on the biological indices (FBI index, Beck Index, BMWP index and Chandler score system (CS)) of macrozoobenthos, water quality in Irtysh River was assessed. The results indicated that the water quality in Irtysh River was characterized as slight pollution. Spearman correction analysis showed that the distribution of aquatic insects was correlated positively with water transparency. Oligochaeta was correlated positively with salinity, conductivity and total dissolved solid (TDS), and had a negative relation with resistance. There was no significant relationship between the distribution of Mollusca and environmental factors.