Aeolian desertification is a kind of land degradation that is characterized by aeolian activity, resulting from the responses of land ecosystems to climate change and anthropogenic disturbances. The source areas of the Yangtze and Yellow Rivers are typical regions of China's Tibetan Plateau affected by aeolian desertification. We assessed the vulnerability of these areas to aeolian desertification by combining remote sensing with geographical information system technologies. We developed an assessment model with eight indicators, whose weights were determined by the analytical hierarchy process. Employing this model, we analyzed the spatial distribution of vulnerability to aeolian desertification and its changes from 2000 to 2010, and discuss the implications. Overall, low-vulnerability land was the most widespread, accounting for 64%, 62%, and 71% of the total study area in 2000, 2005, and 2010, respectively. The degree of vulnerability showed regional differences. In the source areas of the Yangtze River, land with high or very high vulnerability accounted for 17.4% of this sub-region in 2010, versus 2.6% in the source areas of the Yellow River. In the Zoige Basin, almost all of the land had very low to low vulnerability. To understand the change in vulnerability to aeolian desertification, we calculated an integrated vulnerability index (IVI). This analysis indicated that the vulnerability to aeolian desertification increased from 2000 to 2005 (IVI increased from 2.1709 to 2.2463), and decreased from 2005 to 2010 (IVI decreased from 2.2463 to 2.0057). Increasing regional temperatures appear to be primarily responsible for the change in vulnerability to aeolian desertification throughout the region. The effects of other factors (climatic variation and human activities) differed among the various sub-regions. The implementation of the ecological restoration project has achieved a noticeable effect since 2005. Our results provide empirical support for effort to protect the ecology of this ecologically fragile region.