China’s natural resources administration system has provide a vital guarantee for natural resources use and protection over the past decades as a booster to ecological civilization construction, but it still has shortages in lack of rights and responsibilities and in overlapping of leadership and management, leading to lots of issues in unclear ownership subject of natural resources, fuzzy boundary of right confirmation and insufficient protection of property rights. This paper uses property rights theory to analyze the evolution of China’s natural resources administration system under guideline of “the 14th Five-Year Plan”and “2035 Outlook”, establishes a research framework of “system evolution-issues discussion-approach optimization”, and applies Pigovian tax, Coase Theorem, and new system economics theory to qualitative analysis of the natural resources assets property rights system optimization direction. Its evolution of natural resources administration system shows a clarifying ownership at a trend of separation of ownership and using right. Governments as the administrator of market shall uses power to mark market limit and make marketing rules. System performance is mainly related to the gaming between governments and markets, which may be promoted by optimizing the property rights system of “affiliation-rights & responsibilities-protection-transfer-supervision”. The research concludes that in order to improve the natural resources assets property rights system in our country, we should clarify the property rights, and realize the property rights in the legal subject clearly relying on the regulatory effect of the classification agent system. The content of registration and accounting should be clarified, and the information management platform of natural resources assets should be built to accurately grasp the assets, and use the ecological protection compensation mechanism to support the protection system, strengthen the intensity of protection, guarantee market transactions. Marketized trading platform shall be used to improve the allocating efficiency of natural resources, to transfer asset stock to asset increment. Supervision system shall be improved in all process which limits governmental power lists to avoid governmental monopoly.