Serious ecological crises have emerged in the Asian Water Tower region (17 countries centered on the Qinghai-Tibetan Plateau), making it a major priority and challenge for Asian and even global ecological conservation efforts. Constructing a multi-leveled ecological security pattern (ESP) based on the synergies among multiple ecosystem services (ESs) for this region can enhance the structural integrity, functional stability, and spatial connectivity of ecosystems. Therefore, based on a series of GIS spatial analysis methods, the minimum cumulative resistance model, and the analytic hierarchy process, this study measured the importance of five key ESs focused by Sustainable Development Goal 15 (including water conservation, carbon sequestration, sand fixation, soil conservation, and biodiversity conservation); and took fishnet scale as data calculation unit to construct a hierarchical ESP (including three levels of ecological sources and corridors) to provide evidence-based support for identifying and prioritizing synergistic conservation actions across scales (regions, nations, and basins). Overall, the ESP included a total of 534 sources and 656 corridors. Some key conservation obstacles in the region (e.g., edge effects and several human activities) and corresponding priority actions are provided, such as integrating the ESPs into long-term planning, enhancing the conservation and the restoration of both the extent and the quality of forests (e.g., increasing tree species richness), and increasing collaboration across scales for resource mobilization and synergistic land use.