The northeastern margin of the Qinghai–Tibet Plateau is an ecologically fragile region that faces severe habitat fragmentation, which directly threatens regional biodiversity conservation and ecological security. To address this challenge, this study constructed a hierarchical “source-corridor-node” ecological network for the Gannan Tibetan Autonomous Prefecture by integrating Morphological Spatial Pattern Analysis (MSPA), the Minimum Cumulative Resistance (MCR) model, landscape connectivity assessment, and gravity modeling. The key results are as follows: (1) The Gannan Yellow River Water Source Replenishment Area contains 11 core ecological source regions, which are predominantly located in the southeastern regions of Diebu County and Zhouqu County, covering a total area of 4237.81 km²; (2) Ecological resistance analysis identifies high-resistance zones concentrated in anthropogenically active river valleys and urban belts (e.g., Hezuo urban area, Awanzang Town, and the G213 corridor). Low-resistance zones are predominantly situated in protected ecological enclaves (e.g., Zhagana Geopark and Gahai Wetland Reserve); (3) A total of 55 ecological corridors were identified, with a total length of 4355.77 km. Among these, 26 were classified as key ecological corridors, primarily distributed in Diebu and Zhouqu counties in the eastern part of Gannan Prefecture. These areas feature relatively concentrated ecological sources, and the key corridors play a critical role in connecting isolated ecological patches and maintaining regional ecological connectivity. (4) Across the entire territory of Gannan Prefecture, a total of 81 first-level ecological nodes and 53 second-level ecological nodes were delineated. As the core hub of the regional ecological network in Gannan Prefecture, Diebu County encompasses 60 First-level and 41 Second-level ecological nodes, respectively. The hierarchical “source-corridor-node” ecological network constructed in this study effectively enhances the overall landscape connectivity of the area. This progressive analytical framework—integrating source identification, corridor extraction, and node diagnosis—provides a scientific basis for biodiversity conservation, territorial ecological restoration, and sustainable development in high-altitude ecologically fragile zones.