[Objective] The change trend of vegetation cover in the Three-River headwaters region, and its ecological environment were analyzed, in order to provide a scientific basis for the macro layout and implementation of ecological construction projects in the future. [Methods] Based on MODIS-NDVI, DEM, and meteorological data, the spatio-temporal evolution characteristics and future development trend of vegetation cover in the Three-River Headwaters region from 2001 to 2020 were comprehensively analyzed from multiple perspectives by using the maximum-value composite procedure (MVC), trend analysis, the Hurst index, and other methods. The responses of climate change and human activities to vegetation cover were analyzed by combining partial correlation analysis and multiple regression residual analysis. [Results] ① The vegetation cover of the Three-River headwaters region has increased significantly over the past 20 years, with a growth rate of 2.1%/10 yr. Overall, vegetation cover was high in the southeast and low in the northwest, and gradually decreased from southeast to northwest. ② Vegetation cover in the Three-River headwaters region increased over time, with the area of increasing vegetation cover accounting for 74.59%, of the total area, and the area of decreasing cover accounting for 25.41%. The vegetation in northeast and northwest areas increased significantly, and the areas in South Qumalai, North Zaduo, and Southwest Gande decreased. ③ The reverse characteristics of future changes in vegetation cover in the Three-River headwaters region were more obvious than those in the same direction. The area of continuous improvement accounted for 29.22% of the total area, and the area of improvement to degradation accounted for 45.54%. ④ Temperature and precipitation had positive impacts on vegetation cover in the Three-River headwaters region, and precipitation was the main driving factor. ⑤ The impact of human activities on vegetation cover in the Three-River headwaters region increased over time, and the positive impact was mainly located in the northeast Yellow River basin, south of the Tongtian River in Yangtze River basin, and the southeast part of the Lancang River basin. [Conclusion] The Three River headwaters region is an important area for ecological security in China. Vegetation coverage is greatly affected by climate and human activities. It will be necessary to strengthen regional ecological protection and ecological maintenance.