Seaweed-bivalve polyculture and Integrated Multi-Trophic Aquaculture (IMTA) of seaweed, bivalves, fishes, and sea cucumbers have been conducted in Sanggou Bay for decades, leading the development of eco-farming globally. To understand the dynamic changes of macrobenthos and the health status of benthic habitats in the Sanggou Bay, five surveys of macrobenthos were conducted in different mariculture areas of to understand the impact of aquaculture on the benthic ecosystem from May to September 2019. The community characteristics of macrobenthos, such as species abundance, composition, distribution, and biodiversity were analyzed in different mariculture areas in five surveys, and the health status of the benthic ecosystem in Sanggou Bay was assessed using the AZTI Marine Index (AMBI) and multivariate-AMBI(M-AMBI). A total of 56 species were identified, including 31 Polychaetes, 10 Crustacea, 9 Mollusca, 3 Echinodermata, and 2 species of other taxa. The dominant species were Lumbrinereis sp., Tharyx multifilis, Notomastus latericeus, Mediomastus californiensis, Amaeana occidentalis, Paranthura japonica, Scoloplos sp., Potamocorbula laevis, Glycinde gurjanovae, and Cirolana japonensis. During the breeding period, the community diversity index H' of the shellfish and cage culture areas showed a downward trend, indicating that shellfish and cage culture activities have caused excessive organic particle accumulation in the sediments. The abundance/biomass curves showed that the macrobenthos community structure in the Sanggou Bay breeding area began to be disturbed in July, and was moderately disturbed in August and September. The AMBI and M-AMBI Index analyses showed that the macrobenthic community was not disturbed or slightly disturbed and the benthic habitat health tended to relatively good.