Objective: In this study, an ecosystem health assessment framework and a comprehensive resistance surface were constructed to identify ecological source areas and key nodes in the Sichuan-Yunnan ecological barrier area, aiming to lay a foundation for optimizing the ecological security pattern in the study area and provide a scientific basis for ecological protection and restoration. Method: Based on multi-source basic data in 2021 and the “ecological vigor-organization-resilience-ecosystem services” framework, software such as InVEST, Fragstats, and TerrSet were used to evaluate the spatial distribution of ecosystem health in the study area and determine the optimal ecological source protection plan. The random forest model was adopted to calculate the future land-use development probability, and a comprehensive ecological resistance surface was constructed by combining natural and social factors. The ecological security pattern of the study area was constructed through the circuit theory model. Result: In 2021, there were obvious spatial differentiations in the ecosystem physical health index, vigor, organization, and resilience of the ecosystem in the study area. The average values of the ecosystem physical health index and vitality were 0.533 and 0.546 respectively, showing a distribution pattern of high in the south and low in the north. The high-value areas were mainly distributed in the south, southwest, central, and north regions with diverse ecosystem types, abundant wildlife resources, high vegetation coverage, and sufficient water resources. The physical health and vitality levels in the northwest and east were relatively low. The average value of organization was 0.583. Affected by terrain barriers, the high-value areas were mostly in regions with flat terrain, good traffic connectivity, high vegetation coverage, and traversed by rivers. The low-value areas were concentrated in areas with complex terrains such as the Minshan Mountains, Micang Mountains, Qionglai Mountains, Daliang Mountains, and Gaoligong Mountains. The average value of resilience reached 0.667. The western and northwestern regions exhibited low values due to grassland degradation, salinization, and desertification caused by overgrazing. The areas with developed towns, intensively cultivated land, and lakes were also low values. The distribution of the ecosystem health showed a pattern of low in the west, northwest, east, and southeast and high in the northeast, central, and south. The average value of the comprehensive ecological resistance surface was 32.716, opposing the distribution trend of ecosystem health. The ecological security pattern included 210 ecological source areas with an area of 66 990.64 km2, accounting for 28.28% of the total area. There were 511 ecological corridors with a total length of 5 951.475 km, showing a dense distribution in the west and sparse in the east. The general ecological corridors (250) were long and scattered, connecting relatively distant ecological sources. The important ecological corridors (178) were short and densely distributed, forming a corridor network with general corridors. The core ecological corridors (83) connected large-area source areas. A total of 143 ecological pinch-points and 248 ecological barrier points were identified, primarily distributed on general ecological corridors, with land uses mainly consisting of grasslands, other land uses and cultivated land. Conclusion: This study reveals the regional differences in the physical health, and the overall distribution pattern of the ecosystem health is “high in the north and south, low in the east and west”. The northeast, central, and south regions are the concentrated distribution areas of ecological source areas and pinch points, and the integrity of natural vegetation should be protected as a priority. The Aba Prefecture, Ganzi Prefecture, and Shangri-La region are significantly affected by natural factors and human activities and should be preferentially restored. Additionally, spatial planning of the northeast and south regions should be further optimized to coordinate the sustainable development of the ecosystem and the economy.