As increasing attention has recently been paid to the structure and function of the water ecosystems, the ecological function of free\|living heterotrophic flagellates in water ecosystems has emerged as a central issue in water ecological research. Researches have shown that heterotrophic flagellates are being important members of microbial food webs. Strengthen and expand the researches on heterotrophic flagellate diversity, community structure and their function in nutrient recycling will contribute to understanding on the structure, function and the process of water ecosystems. In this paper, species diversity, community structure and feeding ecology of heterotrophic flagellate were summarized. The mechanism in nutrient recycling and the function in water ecosystem of heterotrophic flagellate were also discussed.