Abstract: Species richness is an important metric for assessing ecosystem health, and the species number is one of the most widely used metrics. Fishes are an important component of freshwater ecosystems. Due to their sensitivity to habitat degradation and other environmental stressors, the use of fish as biological indicators has grown in popularity since the inception of Karr’s Index of Biotic Integrity (IBI) in 1981. Based on the analysis of fish diversity in the Yangtze River, we proposed a fish-based ecological assessment systems for the Yangtze River, including the number of indigenous fish species and the number of rare and endemic fish species. The evaluation grades and scoring criteria of each matric was also provided according to the IBI method. Within this framework, we evaluated the ecological condition of the Yangtze River in 2010 and 2020. The results showed that the current ecological environment of the upper and lower reaches of the Yangtze River is better than that of the middle reach. The evaluation grade of Chishui River was “good”, while the Poyang Lake was “fair”. Overall, the ecological environment of the mainstream of the Yangtze River has improved to varying degrees with the implementation of ecological protection measures such as 10-year fishing ban. On this basis, countermeasures and suggestions for further improving the ecological environment of the Yangtze River have been proposed.