【Objective】Identifying the multifunctional status and hierarchical structure of national nature reserves in Yunnan Province can clarify their functional effectiveness and optimization paths while also providing ideas for establishing the spatial layout and cluster management of the nature reserve system, with national parks as the primary focus.【Method】Based on the functional evaluation system constructed using the pressure-state-response model, which considered the 20 national nature reserves distributed in Yunnan Province as subjects. The entropy value method was utilized to classify the functional levels. At the same time, the order-size law and the coupling coordination degree model were applied to analyze the structure of the functional levels and summarized the types of functional structures. 【Result】The national nature reserves in Yunnan Province exhibited inconsistent progress in their current roles, necessitating a coordinated evolution of these functions. The Zipf index indicated that the functions of Yunnan Province's national nature reserves align with the principle of positional order scale, characterized by uniform development. However, the functional items did not reach a definitive edge, highlighting the need to create beneficial functional items within a single protected area. The national nature reserves in Yunnan Province demonstrated a more intense coupling, significant state dysfunction, and a singular protected area’s coupling strength function. The extent of coordination among these variations could be categorized into generally developed, generally lagging, and severely lagging types. 【Conclusion】A primary reason for the heterogeneity in the functional structure of the study area is the interplay between ecological context and economic and social conditions. Future work should focus on enhancing the dynamic nature reserve monitoring network at the provincial level, which aligns with the principle of “synthesis and special characteristics”. Better-developed national nature reserves should be utilized as a central point to merge and optimize the construction of national parks by modernizing adjacent nature reserves. This approach aims to foster the orderly development of nature reserve functions in Yunnan Province and facilitate the synergistic building of nature reserves.