Wilderness, as a nature-dominated ecosystem, provides a wide range of ecosystem services to both the natural environment and human society. However, as human activities increasingly threaten wilderness areas, the global extent of wilderness is shrinking at an alarming rate, severely endangering biodiversity conservation, ecosystem integrity, and sustainability. Due to a lack of necessary connectivity, species migration and gene flow are hindered, making it difficult for wilderness areas to maintain corresponding ecological processes and functions. In this study, we integrate Boolean methods and the MaxEnt model to simulate the degree of wilderness in the Western Sichuan Plateau. From the perspective of ecological security patterns, identifies key areas that impede species migration and dispersal. Combining the Marxan model for systematic conservation planning, it delineates, for the first time, the priority protection levels and key ecological conservation areas of wilderness in the Western Sichuan Plateau. The results show: (1) A total of 164 wilderness ecological sources were identified, primarily distributed in the northern, central, and western regions with higher naturalness. The overall spatial distribution is fragmented, exhibiting clear signs of fragmentation and vulnerability to external disturbances and environmental changes. (2) A total of 429 ecological corridors were extracted, spanning 9387.51 km. The central region has a dense corridor network, while the eastern, western, and northwestern parts of the study area have sparse corridors with limited energy flow. Considering both corridor construction costs and ecological benefits, the final ecological corridor area was determined to be approximately 51776.75 km2. Areas with better habitat quality serve as the core regions of ecological corridors in the Western Sichuan Plateau, facilitating species habitation and migration. Due to human production and development activities, the identified ecological pinch points and barriers exhibit relatively high resistance values, hindering species migration and dispersal. Therefore, it is necessary to strengthen green infrastructure construction along major transportation routes. (3) The priority conservation areas for wilderness in the Western Sichuan Plateau are concentrated in regions such as Ruoergai County, Hongyuan County, and Aba County, covering an area of approximately 37.99 × 103 km2. Among these, the primary priority conservation area spans 22.89 × 103 km2, accounting for 9.84% of the total area of the Western Sichuan Plateau. Secondary and tertiary priority conservation areas are mostly distributed adjacent to primary priority areas, covering 3.16 × 103 km2 and 11.94 × 103 km2, respectively. The findings provide scientific support for further improving the ecological conservation system of the Western Sichuan Plateau.