According to the principle of being “derived from the logical structure of the knowledge system and promoted through the integration and application of knowledge”, advancement in interdisciplinary research is one of the three core tasks of the deepening reform of the National Natural Science Fund in the new era. This article takes an international vision by first investigating the disciplinary layout and application guide for the field of earth sciences offered by leading international science foundations and agencies including the National Science Foundation, United States (NSF); National Research Foundation of Korea (NRF); Japan Society for the Promotion of Science; Agence Nationale De Le Recherche; Deutsche Forschungsgemeinschaft (DFG); European Research Council; Australian Research Council; Ministry of Business, Innovation & Employment; and National Natural Science Foundation of China (NSFC). These application guides include categories of guidelines, extensive application codes, and subdivided application codes. Compared with the existing hierarchical structure for application codes in the field of earth sciences at NSFC, the feasibility and necessity of promoting the optimization of the disciplinary layout and reform of application codes are discussed. Then, it is proposed that the disciplinary layout should be based on the current conditions as well as the future developmental needs of China and that the optimization of application codes should consider the needs of both application guidance rationality and management applicability. Moreover, the setting of application codes should include self-consistent disciplines; exhibit stable inheritance; and support services, emerging intersections, and national needs. To optimize the disciplinary layout, improve the basic research capabilities, and account for the scale of basic research teams and human management resources, the application codes need to be optimized on the basis of three key factors: Extensive application codes, subdivided application codes, and intelligent assistance. Only in this way can the core mission of science foundation management reforms be fulfilled and the goal of building a science foundation management system with advanced concepts, standardized systems, fairness, and efficiency be achieved. In the future, NSFC should focus on the differences between basic scientific research conducted by large and small countries, pay more attention to balanced development in the discipline layout, develop basic general research, and comprehensively promote the growth of the earth science fund. During the past two years, under the guidance of clear, overall strategic planning and top-level design, NSFC’s Department of Earth Sciences has deployed multiple major projects by guidelines, such as those for the major basic science projects of the Sichuan-Tibet railway and frontier projects of basic polar science as well as special projects related to 2019-nCoV research, ecological protection and sustainable development of the Yellow River Basin, and deep-time earth science knowledge graphing and knowledge evolution. These established projects have played key roles in enabling NSFC to meet the major national needs and push forward international scientific frontiers. In the future, NSFC should continue to pay significant attention to strategic research and the top-level design of funding deployment. Moreover, the foundation should strengthen the overall consideration of the top-level strategic results of earth sciences and the layout of the science fund. In practice, the focus should be on the promotion of basic scientific research rather than servicing the other needs of different disciplines. By further improving the condensed mechanism and management methods of the major projects of earth sciences, the important role of guidelines in funding effectiveness will be strengthened. This article can provide the necessary international vision and strategic support for the reform of the application codes of NSFC.