[Objective] The dynamic changes of ecological environmental quality in different sub-basins of the Yangtze River from 2001 to 2021, and the impact of different driving factors on it were determined in order to provide a theoretical basis for the coordinated development of an ecological environmental protection strategy and an economic development strategy for the Yangtze River basin. [Methods] Based on MODIS data, the remote sensing ecological index (RSEI) of the Yangtze River basin from May to November (2001 to 2021) was extracted. The dynamics and driving factors of ecological environmental quality in the Yangtze River basin during the past 21 years were analyzed based on RSEI values. [Results] ① The ecological quality of the middle and lower reaches of the Yangtze River basin was higher than the ecological quality of the upper reaches. The ecological quality in the south was higher than in the north. Except for 2006, more than 80% of the study area had ecological quality above the middle level, and the overall ecological level was classified as good. ② The overall change in ecological environmental quality was classified as stable, and the regions with an upward trend in quality included the Wujiang River, the Taihu Lake water system, Yibin to Yichang section, Yibin to Hukou section, and the Jinsha River basin. ③ The main driving factor of RSEI change was the humidity index, followed by temperature indicators. ④ Ecological environmental quality was greatly affected by wind speed. Rising temperatures will lead to deterioration of the ecological environmental quality in the Yangtze River basin, but the temperatures in the Jinsha River basin, Poyang Lake basin, Jialing River basin, and Hukou and the lower main stream areas were conducive to improvement of ecological environmental quality. ⑤ Increasing precipitation was conducive to improvement of ecological environmental quality in most areas. [Conclusion] The overall ecological environmental quality of the Yangtze River basin has not changed during the past 21 years, but the ecological degradation of the Jialing River basin needs to be given attention by the government, and a series of ecological restoration measures should be put forward as soon as possible to prevent further deterioration of the ecological environment.