The assemblage composition and distribution of meiofauna in the Yangtze Estuary and East China Sea were investigated using samples collected from 16 stations (from 26°N to 32°N, 121°E to 126°E) in July 2012. Generally, both the abundance and biomass of meiofauna decreased from the northern to the southern sea area, increased from the inshore to the offshore area, peaked along the about 45 m isobathymetric line, and then decreased to the offshore area. The meiofaunal abundance amounted to (1206±189) ind/10 cm², and the biomass reached (729±170) μg dwt/10 cm². The standing crops of meiofauna were slightly higher in the summer season than those from the same area in spring and in winter, but distinctly lower than those in summer (June 2003). The low standing crops were likely associated with the low food supply, as indicated by the low sediment chlorophyll-a concentration, though no close relationship was observed. Among the eleven main meiofaunal groups sorted, nematodes represented the most abundant group, accounting for 94.1% of the total abundance, followed by copepods (2.7%) and turbellarians (1.2%). In terms of biomass, nematodes and polychaetes accounted for 62.1% and 18.8%, respectively, followed by copepods (8.3%) and turbellarians (6.1%). Spearman correlation analysis showed that the biomass of meiofauna and the abundance of copepods and turbellarians were respectively negatively correlated to the sediment organic nitrogen content, the polychaete abundance was positively correlated with sediment chlorophyll-a concentration and bottom water salinity, while there was no correlation between the nematode standing crops and any environmental factors. BIOENV analysis indicated that the combination of bottom water salinity, sediment water content and total organic nitrogen content best correlated with the meiofaunal communities. Generally, the abundance of meiofauna decreased over the past ten years. Our study revealed a tendency of the meiofauna congregating from the lower to the upper sediments in the study area over the past ten years, to some extent indicating a changing degraded benthic environment. Based on the measurements of 702 nematode individuals from two stations, we obtained an average individual dry weight of 0.281 μg/ind in the inshore station and 0.186 μg/ind in the offshore station, with an average dry weight of 0.214 μg/ind, a value very close to that obtained from two adjacent stations in autumn-winter of 2009. However, the average dry weight varied with stations, and possibly also with seasons. Thus, simple calculation of nematode biomass using the index of 0.4 μg/ind will obviously over-estimate the biomass of nematodes as well as meiofauna.