At present, the theory and methodology of natural capital valuation have not reached a consensus domestically or internationally. This undoubtedly restricts the positive role of natural capital valuation played in the protection of the ecological environment. To address this issue, this paper analyzed the existing literature, including studies on the theoretical basis of value accounting, empirical accounting methods for stocks and flows, and the rationality of natural capital monetization. We found that natural capital valuation research tended to focus on product quantity, lacking exploration of the monetary value of ecological assets. Currently, three methods, including ecosystem type coefficient table, the localized ecological process model, and emergy-equivalent replacement for ecological product value, have been broadly adopted. They have their advantages and disadvantages in terms of precision applicability, application popularization, and calculation convenience, all of which need further study. In the end, this paper discussed some of the controversies surrounding the monetary accounting of natural capital. Through the above analysis, the paper puts forward the following conclusions:(1) the concepts related to natural capital have not been unified. The natural capital has a certain scarcity and use value, and capital can be divided into stocks (also known as ecological assets) and flows (also known as ecosystem services). (2) The variety of natural capital valuation techniques leads to poor horizontal comparison of research results. It is necessary to improve the accuracy and comparability of accounting results by standardizing techniques and establishing ecological-environmental resource databases. (3) Compared with the value coefficient method based on ecosystem type and the equivalent substitution method based on non-market valuation, the ecosystem service process method based on local parameters can better reflect the characteristics of local ecological and environmental conditions. The accuracy of evaluation and analysis is higher, and there are more ecological management channels. (4) Although there are still some debates about the theory and practical application of the monetary accounting of natural capital, governments and various organizations have promoted the work of natural capital valuation. The results of the exploratory accounting of natural capital have played a positive role in ecological compensation and restoration policies in various countries.