In aquatic ecosystems, most of the small heterotrophic unicellular eukaryotes had been considered as predators of bacteria. Therefore, their contribution to material transfer from primary production to higher trophic levels has been believed indirect and inefficient through microbial food chain. However, recent studies demonstrate that parasitic fungi of large phytoplankton are dominant groups of this size fraction especially in freshwater systems. In addition, trophic link from fungal zoospores to zooplankton (mycoloop) is discovered, which can paradoxically reduce zooplankton biomass by suppressing parasites and thereby indirectly helping phytoplankton hosts, which are inedible for zooplankton. A new food web model with parasitic fungi demonstrates that parasitic fungi are an important determinant of phytoplankton community composition through decreasing the population size of host species, which enhances the material transfer from small phytoplankton to zooplankton. Moreover, their parasitic life strategy with high growth efficiency is able to achieve efficient material transfer from large phytoplankton to zooplankton via mycoloop. Our model clearly demonstrates that these two features make parasitic fungi a key player for the material transfer from phytoplankton to zooplankton.