The investigation was conducted at four sections of Nanji Islands in February and August 2010. One hundred and twenty five species were indentified, including 72 species of molluscs, 23 of macroalgaes, 13 of carapaces, 10 of annelids, 4 of echinoderms and 3 others. 72 species of macrobenthos were collected in winter and 93 species in summer, the average biomass and inhabit density were 3 941.22±2 870.13 g/m², 1 275.44±749.37ind./m² and 4 521.69±3 473.66 g/m², 2 099.07±1 074.82 ind./m², respectively. The dominant species in different seasons have no significant change. The index of Shannon-Wiener's biodiversity was from 1.62 to 2.95, the average being 2.50±0.46. The Margalef's species richness was from 1.99 to 5.88, the average being 4.81±1.31. The Pielou's evenness was from 0.60 to 0.77, the average being 0.71±0.06. The Simpson's dominance was from 0.71 to 0.92, the average being 0.86±0.08. Upon analysis of the macrobenthos community structure by ABC curve, hierarchical clustering analysis and MDS diagrams, the similarity index of community structure between three rocky sections in different seasons were all higher than 50%, and lower than 10% between the only muddy section in winter and summer. The section in Guoxing'ao has the lowest community structural stability, seriously affected by the activities of fishermen.