Forests are critical ecosystems for environmental regulation and ecological security maintenance, especially at high altitudes that exhibit sensitivity to climate change and human activities. The Qinghai-Tibet Plateau—the world’s largest water tower region—has been breeding many large rivers in Asia where forests play important roles in water regulation and water quality improvement. However, the vulnerability of these forest ecosystems at the regional scale is still largely unknown. Therefore, the aim of this research is to quantitatively assess the temporal–spatial variability of forest vulnerability on the Qinghai-Tibet Plateau to illustrate the capacity of forests to withstand disturbances. Geographic information system (GIS) and the spatial principal component analysis (SPCA) were used to develop a forest vulnerable index (FVI) to assess the vulnerability of forest ecosystems. This research incorporates 15 factors covering the natural context, environmental disturbances, and socioeconomic impact. Results indicate that the measure of vulnerability was unevenly distributed spatially across the study area, and the whole trend has intensified since 2000. The three factors that contribute the most to the vulnerability of natural contexts, environmental disturbances, and human impacts are slope aspect, landslides, and the distance to the farmland, respectively. The vulnerability is higher in forest areas with lower altitudes, steeper slopes, and southerly directions. These evaluation results can be helpful for forest management in high altitude water tower regions in the forms of forest conservation or restoration planning and implementation towards sustainable development goals.