Two surveys were conducted in Sanggou Bay in September and November 2016 to study macrofauna in bivalve-seaweed integrated culture areas and fish cage areas. The community characteristics such as species number, composition, distribution and biodiversity and the relationships between macrofauna and the environmental factors were analyzed to investigate the influence of different aquaculture activities on the macrofauna. A total of 67 species were identified, including 36 Polychaetes, 12 Mollusca, 16 Crustacea and Pycnogonida, and 3 Echinodermata. The dominant macrofauna species in Sanggou Bay are Polychaetes. The absolutely dominant species in bivalve-seaweed integrated culture areas are Chaetozone setosa and Lumbrineris longiforlia, while in fish cage areas that are L. heteropoda and Tharyx multifilis. Biomass and abundance were found the higher in fish cage area in September compared to the values in November, and the lowest values were found in the bivalve-seaweed integrated culture area in September. Biodiversity, which showed a reversed trend, was found highest in the integrated culture area in September and followed by the values in the fish cage area in November and September respectively. Correlations were found between macrobenthic community characteristics and sediment parameters (total organic carbon, total phosphorus, sulfide and oxidation-reduction potential). The macrobenthic community was affected by the large-scale aquaculture activities in Sanggou Bay, and the effect of fish cages culture was stronger.