To elucidate the trophic link between micro- and mesozooplankton in the Amundsen Sea polynya (ASP) and adjacent sea ice zone, we estimated the impact of microzooplankton grazing on major phytoplankton groups, as well as the diet composition, ingestion rate, and prey selectivity of two copepods and Euphausia crystallorophias larvae on microbial communities during the late summer. Phaeocystis antarctica, which was ingested by micro- and mesozooplankton, comprised most phytoplankton biomass. Herbivorous microzooplankton consumed at least half of the phytoplankton production, but the microzooplankton grazing may not contribute strongly to the decline of the phytoplankton bloom. Three mesozooplankton species (Calanoides acutus, Metridia gerlachei, and E. crystallorophias larvae) preferentially grazed on ciliates and heterotrophic dinoflagellates (HDF) with sizes from 20 to >100 µm over phytoplankton. Although microzooplankton comprised only an average of 41.7 ± 3.2% o the total carbon available in the natural prey pool, they accounted for an average of 75.4 ± 2.9% of total carbon ingested by copepods and krill larvae. Heterotrophic food sources made up a substantial proportion of mesozooplankton diets, with strong positive selection for microzooplankton at most locations regardless of phytoplankton size and type. In particular, HDF comprised the major dietary component of mesozooplankton in the study area. The presence of mesozooplankton reduced the grazing pressure on P. antarctica and diatoms through predation on herbivorous microzooplankton. Approximately half of the primary production capacity may have indirectly reached mesozooplankton through microzooplankton consumption. Thus, strongly selective feeding behavior and higher grazing pressure on microzooplankton indicated the importance of microheterotrophic pathways through strong trophic coupling between mesozooplankton and the microbial food web during the decline of phytoplankton bloom. In the highly productive ASP system, food web structure can be classified as multivorous, whereby herbivorous and omnivorous modes both play significant roles in carbon export, enhancing the efficiency of the pelagic food web.