Abstract: Since their establishment, the National Science Foundation of the United States (NSF) and the National Natural Science Foundation of China (NSFC) have played an important role in the development of science and technology and the reform of science and technology system in the two countries. NSF and NSFC were established under the market system and the planning system respectively. A comparative study of their founding processes shows that, on the one hand, both NSF and NSFC were created in the key stage of the scientific research system transformation of the two countries, which were the institutional exploration of government support for science. On the other hand, there are differences in the subject of policy proposals, the problems to be solved, and the alliance and debate in consensus shaping, which reflects the deep social structure of the two countries. In general, the establishment of NSF and NSFC shows the characteristics of "idea first" and "practice first" respectively, and constructs a new way of national support for science under the market system and the planning system, which profoundly changes the relationship between the government and science. "How the government supports science" is not only the core issue in the establishment process of NSF and NSFC, but also an important issue facing the development of all countries, which show the new connotation and characteristic. In the face of the endless frontier of science, to strengthen the national strategic scientific and technological strength, China needs all sectors of society to jointly explore the answer to this question in both theory and practice.