This study investigates the relationship between macrobenthic functional group composition and hypoxia in the Changjiang River estuary and its adjacent sea areas. A total of 82 stations were divided into three areas, named non-hypoxic area, hypoxic area and the Changjiang River, respectively. A total of 256 macrobenthic species were collected, which were divided into five functional groups, including carnivorous, detritivorous, omnivorous, phytophagous, and the planktivorous functional group. A similarity analysis performed on the macrobenthic functional groups of the three zones indicates that the functional group distributions of non-hypoxic and hypoxic zones are not significantly different, whereas the functional group compositions of the Changjiang River estuary and the other two zones are rather different. The results of canonical correspondence analysis reveal that the distribution of macrobenthic functional groups is compounded by various environmental factors, of which dissolved inorganic nitrogen, salinity, and temperature exert a significant effect. Combining the results of previous studies, we speculate that macrobenthos are able to adapt to the occurrence of hypoxia by changing their body morphology, distribution location, and community structure. When the environmental conditions prevent the hypoxia from occurring, persisitent hypoxic zones can recover their marine microbenthic community.