The demarcation of national park boundaries is crucial for comprehensive planning, effective management, and maintaining the integrity of ecosystems and biodiversity. This research uses the proposed ‘Ailaoshan–Wuliangshan’ National Park (AWNP) in Yunnan Province, China, as the study area and adheres to the principles of systematic conservation planning (SCP). It employs the Marxan 2.43, MaxEnt 3.4.4, and InVEST 3.14.2 models to predict suitable distribution areas for key endangered species within the AWNP, identifies core ecological source areas, priority conservation areas, and conservation gaps, and constructs a double boundary protection framework. The study’s findings indicate that the potentially suitable habitats for the major rare and endangered species, as predicted by the MaxEnt model, are predominantly located in the Ailaoshan and Wuliangshan areas, with a smaller portion distributed in the Konglonghe area. The InVEST model assessment of habitat quality revealed that the total area of the core ecological source areas is 4775.26 km2, accounting for 35.34% of the total study area. The Marxan model identified a total area of 1064.22 km2 as priority conservation areas, constituting 7.90% of the total study area. Additionally, it revealed conservation gaps of 302.1 km2, which represent 2.20% of the total area. Ultimately, by integrating biodiversity conservation and ecosystem services, the boundaries of the AWNP were optimized into a double boundary delineation model: the inner boundary, characterized by rigid control, spans an area of 1076.20 km2, while the outer boundary, characterized by elastic management, covers an area of 3056.92 km2. Corresponding management recommendations are proposed for the different areas. The double boundary delineation method proposed in this study can, to a certain extent, reconcile the conflict between biodiversity conservation and resource utilization, providing an appropriate reference for the demarcation and dynamic management of national park boundaries in China.