Abstract: A protected area system, with national parks as the main body, is being established in China to achieve a high level of ecological protection and ecological asset management. It is of great significance to construct an analytical framework for the national park system from the perspective of economic theory, so as to understand the deep logic of national park establishment. According to the typical characteristics of national parks in ecological protection, governmental governance, livelihood conflicts, etc., this paper starts from the dual perspectives of horizontal and vertical power integration, and concentrates on constructing an economic theoretical framework for the institutional reform of national parks. In this theoretical framework, the theoretical logic of ecological conservation integrity, multi-objective conflicts, information disadvantage and information asymmetry, transaction costs of intersectoral coordination, efficiency of intersectoral division of labor, "race to the bottom" in local governments, and internalization of positive externalities is comprehensively considered. Moreover, the economic logic framework of national park system based on cost-effectiveness and cost-benefit analysis is innovatively formed. Accordingly, the Northeast China Tiger and Leopard National Park, the Giant Panda National Park, and the Sanjiangyuan National Park are taken as examples of three different management modes for case analyses under the perspective of economics. On this basis, the changes in the cost-benefit of different national parks are analyzed. Meanwhile, important achievements and major challenges in Chinese national park system are summarized. The key issues that should be dealt with in the construction of the national park system, such as the relationship with the original protected areas, the relationship with local government sectors, and the relationship with the livelihoods of the inhabitants, are analyzed and prospected.