Abstract: The flow regime is regarded to be the key driver of structure and function of riverine ecosystems. To assess eco-hydrological regimes alternation in the lower reaches of Three Gorges reservoir, the change characteristics of flow regime were evaluated by using the Mann-Kendall statistical test, the cumulative departure and moving T detected method based on daily flow series at Yichang gauge station from 1952 to 2014, while the hydrologic regime alteration degree and ecological effect of Three Gorges reservoir on the variation of 32 hydrological indexes were also analyzed by the range of variability approach and hydrologic regime alteration degree method. The results show that annual average flow of the Yangtze River has shown a decreasing trend during 1952 to 2014. Yichang gauge station has an obvious decreasing degree with the confidence degree of 90%. The abrupt junction of annual average flow is 2003 year, which means the significant effect of Three Gorges reservoir on the flow regime. The overall degree of hydrological alternation belongs to moderate alternation. The alternation degree of Yichang gauge station was 61%. Three Gorges reservoir has caused the flow regime alternation of the Yangtze River and altered flow regimes have influenced river habitat alternation, aquatic biodiversity decreases and fish population structure alternation. The study provides a scientific reference for the ecological protection and reservoir eco -operation in the middle and lower reaches of the Yangtze River.