Based on macrobenthos samples collected from 4 survey cruises at 40 research stations in March, May, Sept. and Dec. 2004 in Daya Bay, South China Sea, the community structure of macrobenthos was studied. The result showed that macrobenthos community in Daya Bay can be divided into three groups from the inner bay to the main area of the central bay, the central bay and outer bay. The effect of changes between wet and dry seasons on the macrobenthos community structure in Daya Bay was relatively stronger, although seasonal effect on the overall community structure was small. Daya Bay was shown to be ecologically disturbed and the stability of macrobenthic community was weak. Specifically, the inner bay and main area of the central bay was strongly disturbed and was dominated by Group I community that was characterized as simple low stability and dominated by molluscs. Dominant species were Veremolpa micra and Timoclea scabra. The outer bay received little disturbance and the community was most stable. The community belongs to Group Ⅲ that was dominated by polychaete and characterized as complicated and variable. The community change in the central bay was more complicated, concentrated mainly around Maiban Zhou. Its community structure was strongly affected by human disturbance and largely different from other community groups. Species composition of the group was variable which differed largely between seasons. The stability and resilience of the community is low. The current macrobenthic community in Daya Bay is different from the 1980s′ state with largely different species composition, reduced community stability and complexity. Overall, under human disturbance, the macrobenthos community in Daya Bay, and particularly in the central bay, changed to a totally different structure.