The decomposition of submerged plants such as Potamogeton crispus releases a large amount of nutrients into the water body, which has a negative impact on aquatic ecosystems. To investigate the slowing effect of filter feeding benthic animal, the Hyriopsis cumingii, on the deterioration of water quality after the decomposition of submerged plants, a 45 day experimental chamber simulation experiment was conducted from May to July 2023 using different specifications and densities of clams and seagrass combinations to monitor changes in water quality indicators and phytoplankton community structure. It was found that filtration through the Hyriopsis cumingii can reduce the total nitrogen (TN), total phosphorus (TP), chemical oxygen demand (COD), and chlorophyll a (CHLA) in the water to a certain extent. To investigate the density effect and size effect of its Hyriopsis cumingii, low, medium, and high-density triangular sail clams were released. The experimental results show that different sizes and densities of Hyriopsis cumingii can significantly control the biomass of phytoplankton, and Hyriopsis cumingii have a significant impact on the community structure of phytoplankton. Among them, releasing small-sized (shell length 4 cm) low-density (1 g/L) Hyriopsis cumingii has the best effect on improving water quality and controlling phytoplankton biomass.