ABSTRACT: The size fraction structure of the plankton community and their carbon metabolism characteristics play a pivotal role in the ecological function of aquatic ecosystems. Filter-feeding clams are important aquaculture species in the widely practiced Integrated Multi-Trophic Aquaculture (IMTA) models along coastal China. These clams can exert pronounced ecological effects through their physiological activities; the knowledge of how clams impact the plankton size fraction of the aquaculture systems, however, remains limited. In this study, razor clams were co-cultured in the swimming crabs and kuruma shrimp polyculture system at 4 distinct densities. The chlorophyll a (chl a) content, gross primary production (GPP), net primary production (NPP), and respiration of size-fractioned plankton (macroplankton, microplankton, nanoplankton, picoplankton) were measured. The results showed that picoplankton were the primary contributors to the respiration of the aquaculture systems, and nanoplankton played a significant role in chl a content and GPP. The NPP of nanoplankton exhibited positive values across various systems, while the NPP of picoplankton demonstrated negative values. The respiration, chl a, GPP, and NPP of macroplankton, microplankton, and nanoplankton in the clam high-density polyculture group were significantly lower compared to those in the low-density group, while those of picoplankton exerted an inverse pattern across various systems. Co-culturing razor clams at varying densities under the current experimental conditions significantly decreased the biomass and metabolism of the plankton community, which was primarily mediated through nanoplankton alterations due to the selective gazing of clams. Polyculture of razor clams with high density could drive the miniaturization of the plankton community in the IMTA systems.