A quantitative survey to determine the composition of the macrobenthic communities in the southern Yellow Sea was conducted in April 2011. Over 100 species of macrobenthos were identified. Twenty dominant species, belonging to 17 families, 3 classes and 3 phyla, were determined via rank abundance curve analysis. Surface deposit feeding, motile, jawed feeders (27.6%) were the feeding group with the highest relative abundance values, while surface deposit feeding, sessile, tentaculate feeders were the least abundant (1%). The Yellow Sea Cold Water Mass benthic community was dominated by both carnivorous, motile, non-jawed species and carnivorous, motile, jawed feeders, making up 32.3% and 29.7% of the community composition. In the Mixed community the trophic groups were dominated by both surface deposit feeding, motile, jawed and burrowing, motile, non-jawed feeders (46% and 30%, respectively). Surface deposit feeding, motile, jawed feeders (32.8%) was the most abundant macrobenthos category in the Eurythermal community, while in the Yangtze River Estuary community burrowing, motile, non-jawed and surface deposit-feeding, motile, non-jawed feeders represented 43.8% and 31.3% of the total abundance, respectively. The Shannon-Wiener Niche Breadth index, the Pianka Niche Overlap index, the outlying mean index (OMI) and the tolerance index (TOL) were used to analyze the relationships of the dominant species and environmental factors. Four indices were significantly different among species. Thyasira tokunagai, Onuphis geophiliformis, Nine palmata, Ophiura sarsii vadicola, Ehlersileanira hwanghaiensis and Glycinde gurjanovae had large niche breadths. The OMI varied from 0.23 to 4.95. Paralacydonia paradoxa and Glycera tenuis had higher values of OMI (4.95 and 4.78) than that of any other species and the most marginal niche positions of all the dominant species examined. N. palmata (0.23) and Kuwaita heteropoda (0.38) had relatively non-marginal niche positions, and occurred in average conditions across the sampled sites. The tolerance index ranged from 0.13 to 3.85. Sigambra bassi (3.85), Nephtys oligobranchia (2.46) and E. hwanghaiensis (2.25) were the main contributors to the tolerance index. OMI analysis indicated that two species with lower tolerances (narrower niche breadths; more specialized species) were G. tenuis and Paramphicteis angustifolia. Niche overlaps varied from 0 to 0.95. Scoletoma longifolia and N. palmata had a niche overlap value close to 0.95. The significance of the OMI analysis random permutation test demonstrates that niche segregation of Glycera chirori, G. tenuis, Notomastus latericeus, Ophelina acuminate and O. sarsii vadicola is effective along a given environmental gradient (e.g., depth, water bottom temperature, salinity, median sediment size, total organic carbon and total nitrogen). Using hierarchical clustering (CLUSTER) with between-group linkage and non-metric multidimensional scaling (NMDS), the 20 dominant species were classified into three groups: generalist species, typical habitat species and specialist species. We also used Principal Coordinates Analysis to visualize the distribution patterns of dominant species in different habitats. Niche breadth and niche overlap of each species were strongly related to functional feeding groups, habit/behaviors of species, spatial distribution, species abundance and habitat conditions. This reveals the differing abilities of species to effectively utilize their environmental resources.