A quantitative study on the community structure and biodiversity of free-living marine nematodes and their relationship with environmental factors in the northern South China Sea were carried out based on the samples collected at five stations in the deep sea (from 313 to 1 600 m) and one station in shallow waters (87 m) during the cruise in September, 2010. Results showed that the abundance of marine nematodes ranged from 224 to 1 996 ind./(10 cm2). A total of 69 free-living marine nematode genera, belonging to 26 families and three orders, were identified. The most dominant genera were Sabatieria, Linhystera, Aegialoalaimus and Daptonema according to SIMPER analysis. Results of CLUSTER analysis revealed four types of marine nematode community (or station groups) in the sampling area. In terms of trophic structure, non-selective deposit feeders (1B) and selective deposit feeders (1A) were the dominant trophic types with highest genera numbers and abundances, which implied that organic detritus was the main food source of marine nematodes in the northern South China Sea. The percentage of male nematode was low, ranging from 2.22% to 17.81%, while those of juvenile individuals ranged from 36.99% to 82.09%. For genera level diversity of marine nematodes, Shannon-Wiener diversity indices (H’) ranged from 3.76 to 4.57 and had highly significant negative correlation with water depth. In general, diversity indices H’ at the five stations in deep sea (over 200 m) were lower than that at the station in shallow waters (87 m). BIOENV analysis showed that the most important environmental factor controlling marine nematode communities was water depth.