One of the major tasks in the reform of the National Natural Science Foundation of China during the new period is to sort out the knowledge system and optimize the discipline layout after finishing the adjustment of application codes. Based on the 14th Five-year Geosciences Development Plan of the National Natural Science Foundation of China, we propose a new discipline layout for the geological sciences (GS) in China. GS should focus on the prior fields and core scientific questions of “Earth system sciences and deep earth, deep sea, and deep space”, and in their respective sub-disciplines. While preserving essential traditional codes within these disciplines, we suggested to obsolete or merge outdated codes and raise special attention to new-rising subjects or interdisciplinary. According to the sub-disciplines’ characteristics, the geological sciences could be divided into four categories, i.e., basic, applied, cutting-edge and interdisciplinary subjects, and technology supporting subjects. Under the Earth system sciences framework, the authors suggest focusing on the core of basic disciplines, enrich applied fields, expand the cutting-edge and interdisciplinary disciplines, strengthen technological support, and promote a balanced development of sub-disciplines. Based on the investigation results of the discipline strategy, important sub-fields and headings of the GS are proposed. The research done at the GS should broaden its international scope and actively answer the major national requirements, with particular attention to crucial scientific problems in social and economic development. In short, the DGS should centralize efforts on the basic scientific research and national strategic needs. Following the development strategy of the Earth system sciences and deep earth, deep sea, and deep space, the authors suggest that improvements of the research ways and methods in the field of geological sciences, interdisciplinary cooperation and integration, promotions of new fields and sub-disciplines are all necessary. It is suggested to focus on the Earth system sciences, and continue to modify and merge the subjects following the guide of “Grand Geology”. More important, the authors suggest utilizing the rich geological resources in China to promote the development of geological sciences, enhance the international cooperation, and accelerate constructing an open geological big data platform.