This paper describes the major features of nematode assemblages collected at 18 stations in the Changjiang River estuary and its adjacent waters and identifies dominant species within communities in relation to environmental parameters. Meiofauna from the Changjiang Estuary and its adjacent waters comprised 21 major taxa of higher categories. Subsamples of nematodes were extracted and identified to the species level. In general, the nematode community structure was similar to that of muddy sublittoral areas world-wide. The most abundant genera were Daptonema, Cobbia, Sabatieria, Dorylaimopsis and Terschellingia, accounting for 50.0%. The studied area exhibited high nematode abundance and high species biodiversity. Measurements of environmental factors were made, including grain size, salinity, temperature, sediment organic matter content, Chl-a and Phaeo-a. Different combinations of environmental variables are responsible for the meiofauna and nematode communities' structures. However, BIOENV results indicate that water depth, salinity, Chl-a, Phaeo-a and silt–clay content were more closely linked to variation in meiofauna (mainly nematode) community structure in the studied area. Among these, water depth, salinity, Chl-a and Phaeo-a were most responsible for nematode assemblage discrimination in the studied area.