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•We conducted multi-level analyses of protected areas (PA) in effectiveness.•PAs in the Three-river Source Region is effective for biodiversity and ecosystem services.•The soil retention service of the PAs has been slightly reduced.•The stricter the management, the more effective the protection.•Ecological engineering plays a positive effect on the conservation.
Protected areas are widely recognized as crucial for biodiversity conservation and ecosystem service maintenance. In recent decades, countries worldwide have made great progress in expanding the scope of protected areas. However, the evaluation of conservation effectiveness is insufficient due to limited resource inputs. In this study, we assessed the nature reserves’ effectiveness in conserving biodiversity and ecosystem services for the Three-river Source of the Tibetan Plateau in China over the past 20 years at multiple scales. Our findings revealed substantial improvements in biodiversity value, habitat quality, water retention carbon storage, and a slight decline in soil retention. Furthermore, implementing conservation measures within the nature reserves has resulted in better ecological conditions than areas outside. In terms of the different protection zones within the nature reserves, the core areas showed the highest improvement in ecological conditions, followed by the buffer areas and experimental areas. These results indicate a positive influence of ecological projects on conservation objectives. Additionally, the study indicated the effectiveness of more stringent conservation management. Limiting human activities and taking measures to protect soil retention in the Three-river nature reserves is urgent.