Abstract: The development of China′s protected area system in national parks is progressing steadily and entering a critical transition phase from "framework construction" to "quality enhancement". However, the non-coupling contradictions between the protected area system and the administrative regions, manifesting in institutional mechanisms and administrative management, are constraining the full realization of its intended outcomes. Prominent issues include overlapping powers and responsibilities due to an imperfect management system, imbalances between conservation and utilization caused by an inadequate institutional framework, and insufficient institutional guarantees resulting from lagging legal development. These challenges have become key bottlenecks hindering the successful achievement of the protected area system′s goals. Therefore, a thorough analysis of the non-coupling characteristics between protected areas and administrative regions, and the exploration of coordination mechanisms, are of great significance for accelerating the development of China′s protected area system. This paper systematically examines the non-coupling phenomena between protected area management and administrative governance from the perspectives of governance systems, authority allocation, funding investment and expenditure, and legal frameworks. Based on China′s administrative logic combining vertical "lines" and horizontal "blocks" regional governments, this study reveals the underlying causes of non-coupling contradictions, such as fragmented departmental and regional governance, overlapping powers and responsibilities, and conflicting interests. The research indicates that, within these vertical and horizontal dimensions, there exist conflicts between conservation and development goals, contradictions between the generality and specificity of management approaches, and divergences in local interests. Further analysis demonstrates that spatial governance of protected areas faces multiple challenges, including unclear division of authority, poor coordination between institutional setups and local governments, disconnects in the legal system, and the separation of protected area from regional development. According to China′s national context, this paper proposes the establishment of a social-ecological network governance system. This system treats protected areas as ecological nodes, effectively connected via ecological corridors, and governance actors as social nodes, interlinked through collaborative relationships, ultimately weaving an integrated administrative and spatial governance network. By effectively linking social nodes with ecological nodes, a protected area social-ecological network is established. By leveraging collaborative governance to address scale mismatches, a coordination mechanism characterized by "vertical integration and horizontal linkage" can be formed. Specific policy recommendations encompass four areas: promoting coordinated planning, unifying funding allocation, optimizing organizational structures, and strengthening legal safeguards. The study suggests that by innovating governance models, clarifying authority divisions, advancing cross-regional legislation, and enhancing public participation, the coupled development of the protected area system and administrative regions can be achieved. This will facilitate the transition of protected area management from "framework construction" to "quality enhancement", and provide theoretical support and practical guidance for resolving non-coupling contradictions and promoting the sustainable and healthy development of China′s protected area system. Ultimately, it offers a solid institutional foundation and a viable pathway for realizing ecological conservation and coordinated regional development.