There are obvious differences among the upper, middle, and lower reaches in the natural environment in the Yangtze River Basin. The regional topography and climatic conditions are significantly distinct, and economic development is unbalanced. The impacts of various socioeconomic factors, policies, and natural factors on land use stimulate changes in the ecological environment. Therefore, knowledge of the ecosystem's patterns, characteristics, and driving forces is the basis for studying the ecosystem services, ecological environmental problems, and ecological risk assessments. The ecosystem patterns, changing characteristics, and primary driving forces were analyzed from 2000 to 2015 in the Yangtze River Basin. During the 15-year period, about 6.4×10⁴ km² of the ecosystem changed, including a 67.5% increase in urban land, 2.1% increase in forest growth, and 7.5% reduction in croplands. These dramatic changes were concentrated in the lower reaches, big cities in the upper and the middle reaches, urban agglomerations, and reforested cropland areas. Ecosystem patterns and compositions in the upper, middle, and lower reaches were different. Forests and wetlands in the upper reach and urban land in the lower reach increased significantly, whereas croplands and wetlands in the lower reach decreased substantially. Through the analysis of landscape patterns, the degree of landscape fragmentation, as well as landscape diversity, increased. Between the years 2000 and 2015, the change in ecosystem patterns in the Yangtze River Basin was influenced by urbanization, ecological conservation and restoration, water resource development, agricultural development, geological hazards, and climate change. The contributions of the primary driving forces to ecosystem changes varied for the upper, middle, and lower reaches. The first important driving force was urbanization, with a contribution rate of 48.0% and up to 64.5% in the lower reach. The second important driving force was ecological conservation projects, with a contribution rate of 32.8% and up to 47.8% in the upper reach. Water resource development and agricultural development contributed 8.5% and 9.9%, respectively. In addition, the area of plateau lakes increased due to climate change. To sustainably protect the ecosystem in the Yangtze River Basin, the design of the ecological conservation redlines, reasonable land use planning in urbanization, conservation of high quality cropland, and the prohibition of development on important wetlands are necessary.