We investigated the assemblage composition, abundance, biomass and spatial distribution of meiobenthos in relation to benthic environmental variables at 19 stations in the Yangtze (Changjiang) Estuary and its adjacent waters in the East China Sea from November to December 2009. The average abundance of meiobenthos was (1081±700) ind/10 cm² and the biomass was (600±374) μg dwt/10 cm². There was an overall trend in both the abundance and biomass decreasing from the north to the south sea area and from the inshore to the offshore area. Moreover, the abundance was markedly higher in the dilution zone of the Yangtze River than that in the surrounding offshore area. The standing crops of meiobenthos were similar to those obtained from the same area in spring (from April to May 2007), but distinctly lower than those in summer (June 2003). Among the 12 meiobenthos assemblages identified, nematodes were most abundant, accounting for 94.4% of the total abundance, followed by turbellarians (2.3%) and copepods (2.0%). In terms of biomass, nematodes accounted for 68.1%, and followed by turbellarians (14.8%), copepods (6.8%) and polychaetes (5.8%). There were about 70.8% of the total meiobenthos individuals and 69.9% of the nematodes distributed in the surface 0-2 cm sediment layer. These proportions were higher than those recorded in this area (from 54% to 65%). Spearman correlation analysis showed that meiobenthos abundance was positively correlated with sediment chlorophyll-a concentration, and negatively correlated with water depth, bottom water temperature and bottom water salinity. BIOENV analysis suggested that the combination of environmental variables that best correlated with meiobenthos communities consisted of water depth and sediment phaeophytin-a concentration. Our data indicated that the abundance ratio of nematodes to copepods (N/C) generally coincided with the benthic environmental condition in the study area. However, differences in sediment types might discredit the use of this ratio in environmental assessment. Based on the biovolume calculation of 639 individuals from two stations, we obtained the average individual dry weight of nematodes which was 0.104 μg/ind and 0.365 μg/ind, respectively. Our study indicates that the average individual dry weight of 0.4 μg/ind, which has been widely used domestically to calculate the biomass of nematodes, might more or less over-estimate the true biomass.