Coordinating the conflict between protected areas and human activities in Tibet Plateau is one of the key issues that need to be solved urgently in the construction of China’s protected area system. This paper analyzes the relationship between protected areas and human activities，takes the Yarlung Zangbo Grand Canyon National Nature Reserve，the core of the proposed area of The Brahmaputra Grand Canyon National Park，as a research case，and analyzes evolution process，classification and characterization of the conflicts，so as to seek optimal paths for coordinating conflicts in the institutional reform of national park construction. The study found that under different institutional spaces，the relationship between protected areas and human activities is different，which can be manifested as two kinds of relationships：conflict and interest；the relationship between the Yarlung Zangbo Grand Canyon National Nature Reserve and human activities has undergone a process of potential confrontation，cognitive intervention and conflict intention. Using the methods of boundary demarcation and functional zoning，spatial regulation in terms of industry，urbanization and border control are carried out，so as to form a new institutional space and provide a favorable foundation for green development of the protected area.