Samples of subtidal macrobenthic fauna were collected and environmental factors were measured in the Yangtze River Estuary in April, 2005. The community structure of macrobenthic fauna and its correlation with environmental factors were analyzed. Thirty-eight species were identified, belonging to five ecological assemblages. The total species numbers were low, but were higher in the outer sampling sites of the estuary. The average abundance was 32.9 ind./m2 and the average biomass was 5.035 g/m2 (fresh weight) at all sampling stations. Compared with historic data from the 1970s and 1980s, the community structure of macrobenthic fauna has changed obviously and the biomass has decreased rapidly. Total abundance and biomass of the species were obvious higher at the outer sampling sites of the estuary. Salinity was the main factor affecting the distribution of the macrobenthic fauna. The distribution of the macrobenthic fauna communities corresponded to three structural orders of the Yangtze River Estuary.