The upper reaches of the Yangtze River is an important ecological security barrier and water conservation area of the Yangtze River basin, bearing the major national strategies such as Development of the West Regions and development of the Yangtze River Economic Belt. It is important to understand the status of ecological environment and ecosystem services in the upper reaches of the Yangtze River in the past 20 years. Based on ground and remote sensing data, combined with GIS analysis and the model simulation, we calculated the spatio-temporal changes of ecosystem macro-structure, ecosystem quality and ecosystem services in the upper reaches of the Yangtze River from 2000 to 2019, and quantitatively evaluated the trade-offs and synergies of ecosystem services by using correlation analysis, then discussed the impact of ecosystem change on ecosystem services. The results showed that:(1) from 2000 to 2015, the area of settlement ecosystem in the upper reaches of the Yangtze River increased significantly, with an increased of 239.39%. The area of farmland and desert ecosystem decreased significantly, decreased by 5.27% and 21.09%, respectively. The ecosystem was mainly conversion between grassland, forest and farmland. (2) From 2000 to 2019, the ecosystem quality and ecosystem services in the upper reaches of the Yangtze River improved steadily, but deteriorated in some regions. The areas with average FVC greater than 60% accounted for 82.19% in the upper Reaches of the Yangtze River, and FVC showed an increasing trend. The carbon sequestration of vegetation increased as a whole, but decreased locally, with an annual increase rate of 1.65 Tg/a. The soil conservation showed a trend of fluctuating upward, with an annual increasing rate of 2.20 t hm^-2 a^-1. The water conservation showed a trend of slight downward, and some of them varied greatly from year to year. (3) In the upper reaches of the Yangtze River, there were synergistic relationships between carbon sequestration and soil conservation, water conservation and soil conservation. The synergistic relationships between carbon sequestration and soil conservation were mainly distributed in the western of Qinling Mountains, Sichuan Basin and the eastern of Yunnan-Guizhou Plateau. The synergistic relationships between water conservation and soil conservation were mainly located in the eastern of the Qinghai-Tibet Plateau, the western of the Qinling Mountains and the southern of the Daba Mountain. The trade-off and synergistic relationships between carbon sequestration and water conservation were similar, and the trade-off of ecosystem services were mainly located in the Hengduan Mountains and part of Yunnan-Guizhou Plateau.(4) Climate was the dominant factor in changes of ecosystem services, while human activities (ecological projects or urban expansion) affected increases or decreases functions of ecosystem services, and ultimately changed the trade-off and synergy among ecosystem services.