In the recent 30 years, cyanobacterial blooming has occurred frequently in lakes of the Yangtze river basin, especially in Lake Taihu, Chaohu, and Dianchi, which has severely affected the functioning of these lake ecosystems. Cyanobacterial blooming in lakes has certainly become a major challenge to the sustainable development of regional economy in China, which needs urgent solutions. Although the environmental problems generated by cyanobacterial blooming has got more and more attention, the mechanism of ecological catastrophe driven by the blooming is unclear until now. Most studies have been focusing on the occurrence of cyanobacterial blooms in the last decades. The current project aims to reveal the mechanism of ecological catastrophe induced from cyanobacterial blooms and to find practical means to control the negative impacts. Three key questions will be addressed in this project, which include: ①development, environmental process, fate, and toxicological effects of pollutants derived from cyanobacterial blooms; ②regime shift and functional change of lake ecosystems induced by cyanobacterial blooms; ③evaluation and control mechanism of ecological catastrophe caused by the blooms. Lake Taihu, Chaohu, and Dianchi will be chosen for a comprehensive and comparative study. The project will focus on the pollution mechanisms of cyanobacterial blooms, subsequent response of lake ecosystems, and thus the corresponding means reducing these negative impacts. Major research contents include the formation, environmental process, and fate of derivate pollutants from cyanobacterial blooms, ecotoxicological effect of major pollutants and safety of water quality, key process and change of lake ecosystems in response to cyanobacterial blooming. Based on these studies, new methods and principles for reducing the negative impacts will be studied and promoted. This study will finally have implications for ensuring the safety of regional ecology and sustainable development of regional economy. This study may also have contributions to the knowledge about ecology of keynote species, ecological resilience and catastrophic ecology.