Megabenthos samples were collected using 10-min trawls towed at 17 stations from 2015 to 2016. The dominant species (>1% of the total density) were Stegophiura sterea (10.4%) and two subtropical species, Mactrinula dolabrata (9.0%) and Acila divaricate (8.3%), respectively. The community structure of the megabenthos fell into four groups: the southeast, the southernmost region off Jeju Island, the frontal zone of the South Sea with C3, and a diagonal area from the south coast to the western side of Jeju Island. The total numbers of species, diversity, density and biomass were higher in the C3 region of the South Sea. Environmental factor analysis showed that differences in the megabenthos community were related to depth, gravel contents, and sorting value (σ). These results indicate that changes in the marine environmental conditions in the South Sea of Korea affect the megabenthos species’ composition and diversity.