The National Natural Science Foundation of China (NSFC) launched the Reform Initiatives, and defined three major reform tasks under the guidance of the overall goal of building a national natural science funding system in the new era. One of the three tasks under this goal is to optimize the funding layout in order to support convergence between knowledge and application according to the inherent logic and landscape of the knowledge systems. The application code system of NSFC is of vital importance to its funding strategy and provides strong guidelines for the disciplinary layout. In 2019, the discipline of atmospheric sciences (DAS) was selected as a reform pilot in the Department of Earth Sciences (DOE) of NSFC. Based on “problem orientation”, the application code system was reviewed and significantly revised according to the top-level strategy of “Habitable Earth”, initiated by DOE. The “Habitable Earth” strategy is dedicated to promote the geosciences within the frame of Earth System Sciences, with emphasis on “deep earth”, “deep sea”, and “deep space”. In this study, the background for the code system adjustment is addressed, the reform idea and measurements are illustrated, and the structures of the new code system are set up, which are helpful for the applicants to select the appropriate codes in their proposals, and beneficial to the scientific community to better understand the future funding layout of DAS. After in-depth analysis of previous application code system, several key drawbacks are pointed out. They are but not limited to: (1) Lack of self-consistency in logical structures, (2) incomplete coverage of sub-disciplines, and (3) disconnection with the strategy of “Habitable Earth”. To address these issues, this paper proposes a new classification strategy for the application codes according to three coordinated aspects: (1) Branch disciplines, (2) supporting technologies, and (3) social development services. The effective promotion of the integration of atmospheric sciences within “Habitable Earth” is proposed by establishing cross-disciplinary codes for interdisciplinary sciences. The proposed new code system in DAS consists of 15 sub-codes, i.e., “D0501 Synoptic Meteorology”, “D0502 Climate and Climate System”, “D0503 Paleoclimatology”, “D0504 Atmospheric Dynamics”, “D0505 Atmospheric Physics”, “D0506 Atmospheric Chemistry”, “D0507 Ecological Meteorology”, “D0508 Planetary Atmosphere”, “D0509 Atmospheric Observation Techniques”, “D0510 Atmospheric Data and Information Science”, “D0511 Atmospheric Numerical Model Development”, “D0512 Earth System Model Development”, “D0513 Climate Change, its Impacts and Countermeasures”, “D0514 Atmospheric Environment and Medical Meteorology”, and “D0515 Applied Meteorology”. The first eight items (D0501 to D0508), the next four items (D0509 to D0512), and the last three items (D0513 to D0515) are categorized as “branch disciplines”, “supporting technologies”, and “social development services”, respectively. Based on the adjusted application code system, the “research directions” for each code as well as “keywords” for each direction are determined. Finally, a complete information chain for the discipline of atmospheric sciences is formed, consisting of “application codes”, “research directions”, and “keywords”. The expert information in the DAS database has begun to be updated according to the new chain. The information in the new chain will be also conducive to the application of artificial intelligence technology in assigning the proposals to appropriate reviewers and classifying the research achievements in DAS. The efforts to adjust the application codes reflect the consensus of the broad atmospheric sciences community on the development of atmospheric sciences from “traditional meteorology” to the concept of “Habitable Earth”, as well as embody NSFC’s funding orientation in the new era of China.