Bivalve-macroalgae polyculture (BMP) is one of the most important aquacultural means and can maintain a nutrient balance and prevent eutrophication in aquaculture waters. Sansha Bay is a typical mariculture bay on the coasts of southeastern China. The quantity of BMP has expanded in recent decades, while the ecological functions and risks of intensive BMP remain unknown. This study compared the food web structure and ecosystem characteristics between 2010 and 2019 using Ecopath and simulated individual and combined effects of BMP on the ecosystem to detect the ecological functions of polyculture using Ecosim. The results showed that with the expansion of aquaculture in Sansha Bay during the last decade (2010–2019), the total biomass (492.82 g/m 2 /a) and total flow (19,553.75 g/m 2 /a) of the ecosystem in 2019 were higher, while the contribution of phytoplankton to primary production accounted for only 13.5%. In Sansha Bay, the total transfer efficiencies were lower than in other aquaculture ecosystems, 4.16% and 4.27% in 2010 and 2019, respectively. The maturity declined slightly, and the ecosystem's primary productivity was still redundant in Sansha Bay based on the analysis of ecological characteristics. The biomass of phytoplankton increased more than two times to remove BMP, which indicated the positive control of eutrophication and harmful algae blooms. However, each culture species should be scientifically evaluated to reduce the redundancy of the ecosystem, improve the system's maturity, and make the aquaculture ecosystem more resilient and stable. • Expansive bivalve-macroalgae polyculture is a double-edged sword. • BMP pattern effectively controls eutrophication and HABs in the aquaculture ecosystem. • Expansive BMP increases the redundancy and ecological risks of aquaculture ecosystem. • The potential risks of expansive macroalgal culture should be paying more attention. • EwE is a useful tool for diagnosing the ecological risks of the aquaculture ecosystem.