Abstract: As an indispensable natural resource for human survival and social development, mineral resources play an important role in promoting the great rejuvenation of the Chinese nation with Chinese-style modernization. In order to implement the overall deployment of the ecological civilization system reform of the Party Central Committee and the State Council, comprehensively promote the reform of the property rights system of natural resources assets, and implement the unified exercise of the responsibilities of the owners of all natural resources assets, this paper, on the basis of in-depth understanding of the requirements of Chinese-style modernization for the management of natural resources assets, sorts out the requirements of the pilot scheme of the principal-agent mechanism for the ownership of mineral resources assets, and puts forward the significance of establishing a cost expenditure compensation mechanism. Based on the perspective of the owner and equity management of mineral resources assets under the principal-agent mechanism, the connotation of income, cost and cost expenditure compensation of mineral resources assets is defined. Taking Inner Mongolia as the research scope, based on a comprehensive review of the current situation of mineral resources asset management and income and expenditure, the status and existing problems of asset income and expenditure are analyzed. The logical relationship between income, cost and cost expenditure compensation of mineral resources assets is fully considered. According to the central and local powers corresponding to mineral resources in the list of natural resources, the principle of adapting power, expenditure responsibility and financial resources and giving priority to the income of mineral resources assets is directly used to compensate for reasonable cost expenditure. This paper puts forward some suggestions on the compensation system of mineral resources assets cost, which provides a reference for Inner Mongolia to establish the cost expenditure compensation mechanism of mineral resources assets, and provides a basis for improving the management system of natural resources assets.