As an important part of earth sciences, marine sciences are closely related to economic and social development, marine security, and global change. They are a source of knowledge for earth system sciences, an important basis for sustainable development, and underpin strategies of maritime power. This paper summarizes trends in the development of marine sciences and their main challenges in China. It is important to establish a sound subdiscipline of marine sciences to carry out original work, to obtain basic theoretical data, and to innovate for future development. The paper describes the trends in marine science funding allocation, and details some of the leading national basic marine science research around the world to provide context for the development of marine sciences in China. The paper reviews the succession process of basic research funding allocation. The discipline application code system of the National Natural Science Foundation of China (NSFC), as the important framework of NSFC funding, determines the development of marine science research. It must be continuously updated and developed in accordance with the rules of development and the requirements of social services. Accurately determining the application codes is essential for the NSFC to allocate funding appropriately. In the 1980s and 1990s, the marine sciences were divided into eight subdisciplines. In 2008, the NSFC carried out a large-scale revision, and the marine sciences were divided into the current 11 subdisciplines. The paper introduces a new application code system for marine sciences and describes its development process. In the last ten years, marine sciences have developed rapidly, and the previous application codes could not adapt to the current development and trends in marine science and technology. Under the unified deployment and guidance of the Department of Earth Sciences of the NSFC, the Oceanography Group launched a systematic demonstration and overall redesign of the application codes of marine sciences in 2018. The aim was to better reflect the systematization, completeness, and progressiveness of the marine sciences system in the new era, to guide the direction of marine science research, and to promote the interdisciplinary, balanced, and coordinated development of marine sciences. Combining “top-down” and “bottom-up” approaches, the group further analyzed the trends in the development of marine science research and carried out a systematic critical review. Considering the current situation and the challenges in achieving the coordinated development of marine science and technology and its social impacts, the group proposed a new version of the system comprising 15 application codes, covering three directions of “Branch Discipline”, “Supporting Technology”, and “Development Field”. “Branch Discipline” comprises six codes: D0601 Physical oceanography, D0602 marine chemistry, D0603 marine geology and geophysics, D0604 biological oceanography and marine biological resources, D0605 marine ecology and environmental science, and D0606 estuarine and coastal science. “Supporting Technology” comprises three codes: D0607 Marine remote sensing, D0608 marine physics, and observation and detection technology, and D0609 marine data science and information system. “Development Field” comprises six codes: D0610 Marine system and global change, D0611 marine engineering and environmental effects, D0612 marine disasters, and disaster prevention and mitigation, D0613 marine energy and resources, D0614 coordinated sea and land development, and sustainable development, and D0615 polar science. The updated system is forward-looking, coordinated, logical, and consistent, and better supports China’s basic marine science and major national requirements. Last but not least, the paper describes the Shiptime Sharing Project to support the Open Cruise Program, as well as an international cooperation network established by the NSFC. The trends in the development of these projects and future prospects are also discussed. The revision of the application codes has comprehensively organized funding for marine sciences in the new era. The new codes specify directions for the development of marine technology, and provide a means for the implementation of the national marine strategy through funding allocation. Basic marine scientific research will be better served by this optimized NSFC marine funding allocation system.