Abstract: The physical integrity of key reaches of the National Nature Reserve for rare and endemic fishes in the uperstream of Yangtze River is assessed in consideration of eight indicators, inclusive of flow process variability, high flow frequency, high flow duration deviation, bank slope stability, habitat type diversity, sediment type diversity, riparian vegetation coverage and vertical permeability. Results show that the physical integrity of the Chishui River is much higher than that of the mainstream Yangtze River. And among the three reaches of mainstream Yangtze River, Jiangjin reach has high physical integrity, followed by Yibin reach and Hejiang reach. Moreover, four indicators (high flow frequency, high flow duration deviation, habitat type diversity, vertical permeability) vary greatly before and after the impoundment of Xiangjiaba dam which affects the hydrological process of the key reaches, especially the indicators of pulse flow and its duration, median diameter in sediment, and distribution of water depth and velocity.