Pearl River Delta is one of the main aquaculture areas in China. In order to understand the community structures of macrozoobenthos and further assess the water quality in aquaculture ponds, a field investigation of macrozoobenthos and environmental parameters was conducted in 30 ponds with six aquaculture models during July to August 2016. The results showed that a total of 18 species belonging to 14 genera and 3 phyla were identified, and the species number of oligochaeta, aquatic insect, and mollusca was 7, 7, and 4, respectively. The dominant taxa of macrozoobenthos were the Limnodrilus claparedeianus, Limnodrilus sp., and Chironomus sp., which have strong tolerances to pollution. The average species number among the six model ponds had no significant differences. However, the density and biomass were significantly different, and which were significant higher in two models (juvenile and adult fish, respectively) of hybrid snakehead (Channa maculate♀×Channa arguss♂) than the other four model ponds. Pearson correlation analyses showed that the TN and TP were the main factors influencing the density and biomass of macrozoobenthos in aquaculture ponds of Pearl River Delta. The density and biomass of oligochaeta were only positively correlated with TN, while which of chironomids were significantly affected by TN and TP. The water quality of 30 aquaculture ponds were assessed using Shannon-Wiener index, Margalef index, and Biotic index. It suggested that the Shannon-Wiener index was not appropriate for the assessment of water quality in aquaculture ponds of Pearl River Delta. The assessment results by Margalef and Biotic index showed that all the ponds of grass carp (Ctenopharyngodon idellus) and hybrid snakehead were heavily polluted, while most ponds of large mouth bass (Micropterus salmoides) and tilapia (Oreochromis mossambicus) were heavily polluted and a few ponds were moderately polluted.