The Three Rivers Source, known as the “Water Tower of China”, is the birthplace of the Yangtze River, Yellow River, and Lancang River. The carrying capacity and environmental capacity of its ecological environment affect the ecological balance and resource utilization in the surrounding areas of the Three Rivers Source region, and are even closely related to the country’s ecology and economy. Taking the Three Rivers Source region as the research object, this paper selects six indicator layers and their corresponding 23 indicator items that affect the ecological vulnerability of the region. Nine professors in the field of ecological environment were invited to score and screen the indicators. Finally, a judgment matrix was established, and the Analytic Hierarchy Process (AHP) was used to comprehensively evaluate the ecological vulnerability of the Three Rivers Source region. The research results show that the most significant factor affecting the ecological vulnerability of the Three Rivers Source region is the reduction in ecological area, with a weight of up to 23.4%. This factor is followed by changes in terrain, growth and development environment, ground trampling effects, changes in vegetation structure, and potential changes in the integrity of natural vegetation. Their weights are 19.8%, 18.5%, 15.4%, 13.8%, and 12.3%, respectively. The weight of reduction in area is approximately 1.6 times higher than the potential impact on the integrity of natural vegetation. Changes in soil environment and terrain are the primary factors affecting ecological vulnerability. The lower the potential integrity of vegetation, the more fragile the ecosystem. Among the 20 research sites in the Three Rivers Source region, one has an extremely fragile ecological environment, and only six sites do not require excessive intervention. By analyzing and evaluating the different influencing factors of ecological vulnerability in the Three Rivers Source region, this study formulates corresponding ecological strategies to ensure the ecological restoration and sustainable development of the Three Rivers Source region. It provides a theoretical basis for the protection, management, and ecological construction of the Three Rivers Source region.