While the reform of China's protected areas system has contributed to optimizing the overall layout of regional ecosystem services and biodiversity conservation, challenges remain regarding insufficient strategic cooperation among protected areas and with adjacent regions. Using Qinghai-Tibet Plateau (QTP) national park clusters as a case, we analyzed the spatio-temporal characteristics of key ecosystem services including soil conservation, water conservation, sand fixation, and habitat quality, within the QTP national park clusters. From a regional interaction perspective, we conducted cluster analysis to identify regional dominant functional groups and propose management optimization strategies. The results indicate that: (1) the average values of soil conservation, water conservation, and sand fixation within the national park clusters account for 17.31%, 18.18%, and 24.09% of the QTP, respectively, with the average comprehensive ecosystem service index showing a slight annual increase; (2) PCA and K-means clustering, based on ecosystem services, divide the QTP national park clusters into five regional dominant functional groups. These groups are defined as follows: a climate and geopolitical security barrier in the QTP, ecological security for the Hexi Corridor, an international river ecological security barrier, a soil-water conservation barrier, and a sand fixation barrier in the east and northwest of the QTP; (3) we propose recommendations on how to further promote collaboration among dominant functional groups and between them and adjacent regions, as well as to foster social-ecological resilience in the future. This study provides insights for the sustainable management of protected areas and the safeguard of ecological barrier systems on the QTP.