Improving the management system of state-owned natural resource assets (SONRAs) plays an important role in the institutional reform of ecological civilization in China. It is of great significance for promoting the protection of natural resources and effectively safeguarding the owner's equity in their SONRAs. Guizhou Province is one of the first ecological civilization pilot sites in China. In this study, we used field investigation methods and the method of historical documents to obtain materials and data about the management of SONRAs in Guizhou Province, and then systematically analyzed the practices in SONRAs management. On this basis, some remaining problems were identified, such as the uncertainty regarding the amount of SONRAs, poorly-defined ownership of property rights and an imperfect revenue system. In response to these problems, countermeasures and suggestions are proposed for the effective maintenance of the owner's equity in their SONRAs, including establishing an inventory and statistics system to complete the task of comprehensive inventory, establishing an evaluation and accounting system and exploring the path for value realization of ecological products, establishing the principal-agent system and figuring out the asset management listing and agency system, perfecting the income management system to standardize asset income management and improving the asset allocation system to promote the efficiency of resource allocation. The results of this study will provide a reference for strengthening and improving the management of SONRAs in Guizhou Province.