Drought is an extreme event in hydrological water cycle, and it happens in more areas and more frequently, which has significant negative impact of water resources, water environment and ecosystem. The paper discusses the effects of drought on water ecosystem by the drought affected area, hydrological characteristics, drought duration, low flow value, drought season, drought frequency, and droughts-floods abrupt alternation. The effects of drought on aquatic habitats of rivers are discussed, the speed of river flow is slow, the area and depth of aquatic habitat reduced, and the diversity of aquatic organisms in rivers is affected. The effects of drought events on material flow, energy flow and information flow in aquatic ecosystems were analyzed from the following three aspects: longitudinal scale, horizontal scale and vertical scale. We also summarized the relevant research of the hydrological process water ecosystem coupling model. Finally, the research trend and key research work in the future are prospected.