Vegetation change trends and the response of different types of vegetation to climate change were analyzed using spot vegetation Normalized Difference Vegetation Index(NDVI) data from 1998 to 2010, vegetation maps at a scale of 1 ∶ 1000000 and climate data obtained from 16 weather stations in or near to the Three-River Headwaters region. The effectiveness of ecological conservation and construction was also assessed by separating the contribution of human activity from climate factors to vegetation growth. Results show that vegetation in the study area increased in density between 2001 to 2010 at a regional scale and vegetation growth decreased from the southeast to the northwest of the study area. The contribution of climate change and human activity to vegetation growth was calculated at 79.32% and 20.68%, respectively, indicating that change in vegetation is mostly influenced by climate change and enhanced by human activity. Precipitation as well as temperature has a great impact on vegetation change at the study site. Precipitation and temperature during spring and autumn, especially in April and October, are the most important to vegetation growth in the alpine area. The impact of climate change on NDVI differs between vegetation types, with the greatest impact observed in alpine grassland areas over forest and shrub areas. The NDVI of alpine meadow areas correlates strongly with both precipitation and temperature. In alpine steppe areas temperature has more influence on NDVI, while precipitation has a stronger relationship with NDVI in areas of mountain vegetation. Under a changing climate between 2001 to 2010, which promoted vegetation growth because of the increase in precipitation and temperature, human activity was found to have a positive effect on vegetation growth as shown from the calculation of a residual value of 0.0863 between real NDVI and simulated NDVI. This provides evidence that ecological conservation and construction programs have achieved initial success. The most obvious effects occur in the east of the Yellow River source region and the two sides of Tongtian River of Yangtze River source region. In mountain areas such as Tanggula Mountain, Kunlun Mountain and Buqing Mountain, human activity is still found to have negative effects on vegetation growth. The positive effects of human activity on vegetation decreased between 2001 to 2010, as shown from the negative slope of -0.0039. This indicates that most ecological projects are implemented with a short-term design and a lack of long-term planning.