China’s water source includes the headwaters of the Yangtze, Yellow, and Lantsang (the Mekong outside China) rivers and is located in the heart of the Tibet Plateau, which has an average altitude of 4,200 m. Due to the importance of the Water Tower to the ecological security and economic development of China and South Asia, desertification issues in this region have attracted the attention of the public, scholars, government officials, and international organizations. Combined satellite-derived vegetation indices, field surveys, and surface meteorological data to evaluate the effects of climate change, our analyzed results show that during the early part of the twenty-first century, no desertification occurred in these source areas. However, between 2000 and 2010, human activities may have had a negative effect on about 50 % of the region, although vegetation rehabilitation still occurred during this period. Although the Ecological Protection and Restoration Program was launched in China in 2005, the negative impacts of human activities such as agriculture have still increased in the water source. Vegetation rehabilitation in these source areas appears to be driven mainly by the effect of climate change, and it is possible that human activities do not play an important role in regional ecological and environmental evolution. Although at present we cannot determine whether it was rising temperatures or increasing precipitation that enhanced vegetation growth in the region, our results show that the dominant factors controlling vegetation rehabilitation in China’s Water Tower are related to climate.