The establishment of the Sanjiangyuan National Park (SNP) system indicates a higher requirement for refining management practices, especially for protecting the ecological barrier system (EBS) that supports national ecological security and biodiversity. However, it is still understudied how planners can identify the key areas for maintaining EBS in addition to functional zoning. This study took the SNP as an example and built a comprehensive analytical framework, including fragmentation analysis, landscape morphology analysis, and connectivity analysis based on graph theory. The study found that the ecological patches of the Lancang River Source sub-park are relatively complete, while those of the Yangtze River Source sub-park and the Yellow River Source sub-park are more fragmented according to different indicators. The study then identified key nodes and edges of sources for maintaining the EBS. These areas are located mostly near core zones of habitat patches. Furthermore, the study analyzed key patches for maintaining landscape connectivity using two indicators DN (degree of nodes) and dIIC (the delta integral index of connectivity), which respectively quantify the number of neighbors of a habitat and its impact on the whole connecting EBS. Last, the study identified areas with dense landscape corridors in the EBS for suggesting key protection areas.