Optimizing the discipline layout is an important task for deepening the reform of National Natural Science Foundation of China. The discipline of environmental geosciences (DEG) has a short history and is not perfect in the discipline layout and system framework. The DEG takes the opportunity of optimizing the discipline layout and proactively responses to the top-level strategy of “Habitable Earth-Earth System Science”, initiated by the Department of Earth Sciences. Based on a wide range of strategic research, the establishment background of DEG was reviewed, and the challenges of DEG in terms of research objects, theoretical systems, technical methods, and research paradigms were analyzed. The overall concept of optimizing the discipline layout of DEG was clarified, namely basic disciplines, interdisciplinary disciplines, cutting-edge fields, new technologies and methods, and national needs. Based on the overall concept of the discipline layout, the discipline framework of “four beams and eight pillars” was established. Four basic disciplines constitute the “four beams”: Soil science (D0701), environmental water science (D0702), environmental atmospheric science (D0703) and environmental biology (D0704). Four interdisciplinary disciplines and four cutting-edge fields together constitute the “eight pillars”. The four interdisciplinary disciplines include engineering geological environment and disaster (D0705), environmental geology (D0706), environmental geochemistry (D0707) and ecotoxicology (D0708). The four cutting-edge fields are environmental pollutant behavior and environmental effects (D0709), environment and health risks (D0710), quaternary environment (D0711), environmental information and environment forecast (D0712). New technologies and methods of DEG (D0713) are the support of the discipline. Regional environmental quality and safety (D0714) and environmental protection and sustainable development (D0715) are the major objectives of DEG to serve national needs. Combining the characteristics and advantages of DEG to serve national needs, the connotation of DEG is defined as pollution environment, ecological environment, disaster environment and healthy environment. The existing problems of the discipline application codes were identified, including incomplete code system, unsmooth logical relationship between codes, and unbalanced code level and size. The preliminary adjustment proposals for the application codes were put forward. This study is for related researchers to discuss and promote the high-quality development of DEG.