Abstract: Focusing on the “two unifications” responsibilities—that is, the unified exercise of ownership responsibilities over all state-owned natural resource assets, and the unified exercise of responsibilities for territorial space use control, ecological protection, and restoration—this paper analyzes the causes and effects of the blurred distinction between ownership and supervision rights over natural resources. It defines the scope and criteria for exercising these two types of rights and proposes measures to optimize their management. The findings suggest that, in the long term, exploring the establishment of a specialized natural resource asset management agency could enable the unified exercise and management of natural resource asset ownership. In the short term, it is advisable to maintain the current arrangement in which the Ministry of Natural Resources carries out the “two unifications” responsibilities, supported by a coordination mechanism involving relevant central ministries and commissions. Under the system where one department exercises both responsibilities, it is essential to strengthen coordination and cooperation between ownership and supervision rights in key areas, so as to achieve integration, proper positioning, and complementarity between the two. The ownership management system should be improved by refining resource inventories and advancing state-owned asset legislation, thereby clarifying the scope of ownership rights and responsibilities and achieving a clear separation between the two rights. Ownership rights and supervision rights manage the protection, development, and utilization of natural resources from different perspectives, through different methods and means. While they operate independently, overlap, constrain, and supervise one another across different management stages, they are not isolated. Rather, they are interconnected and complementary, ultimately serving the same entity—the people as a whole.