Seasonal hypoxia is a common phenomenon in many estuaries all over the world and the frequency, area, duration and intensity of coastal hypoxia have been increasing in recent years. Thus, more attention has been paid to understand the ecological consequences of hypoxia. Estuaries are the home of many living species that can be classified into plankton, nekton and benthos based on their swim ability and the habitats they live. Estuary hypoxia not only affects the distribution and survival of estuarine organisms, but also changes the community structure and influences the structure and function of ecosystem. This paper summarizes the advances in the research of biological effects of estuary hypoxia from the levels of molecular, community and ecosystem.