Macrozoobenthos community structure in the lower reaches of Ganjiang River was investigated in June (wet season) and November (dry season) 2009 and April (normal-water period) 2010. A total of 25 species from 15 families were recorded. Results showed that temporal and spatial variations of the macrozoobenthos community structure were obvious in the lower reaches of Ganjiang River. The mean maximal density (145.9 ± 81.8 ind./m²) occurred in June while the minimum (89.6 ± 15.9 ind./m²) appeared in April. On the contrary, the mean maximal biomass (90.1 ± 25.4 g/m²) occurred in April while the minimum (62.9 ± 20.9 g/m²) appeared in June. Their mean densities in the main stream were always higher than those in branches. However, the mean biomass in main stream was lower than that in branches in November. Temporal and spatial variations of three indices (including Shannon-Wiener index, Margalef index and Pielou evenness index) were apparent. Maximal values of all the indices occurred in November while the minimum appeared in June. The Shannon-Wiener index and Margalef index in the main stream were lower than those in branches in June and April; however, the Pielou evenness index in branches was constantly higher than that in the main stream, which showed that the community structure of macrozoobenthos in branches was more diversiform, uniform, and stable than that in the main stream. According to Shannon-Wiener index and Margalef index, the lower reaches of Ganjiang River was polluted to a certain extent and the main stream was more serious.