The premise of realizing the ownership rights and interests of national natural resource assets lies in the accurate evaluation of asset value. With the deepening of research, the scope of natural resource asset evaluation has gradually expanded from the initial simple econometric quantity value to the more complex economic-ecological comprehensive value. Therefore, a comprehensive and systematic requirement is put forward for the evaluation of natural resources assets. Based on the requirements and practical exploration of the natural resource principal-agent mechanism, the construction of the natural resource asset value evaluation framework was studied, and the construction of the natural resource asset evaluation framework under the principal-agent purpose of national ownership of all natural resource assets on the basis of clarifying the logical relationship between various evaluation items was exploresd. It is expected to be beneficial to the value accounting and the implementation of the owner’s equity in the later stage of the entrustment of the ownership of natural resources assets.