Taking “science and technology to create a country” as the starting point, and to get rid of its dependence on foreign advanced scientific instruments, the Japanese government has formulated the Development of Advanced Measurement and Analysis Systems, laying a solid research and development foundation for Japanese science and technology. Taking the plan as the research object, this paper makes an in-depth analysis on its introduction background, management structure, field distribution, fund investment and implementation effect using case analysis method, bibliometric method and social network analysis method. By comparing the management process of the natural science foundation of China, it is found that China's national-level scientific research project planning and inter-departmental scientific research projects are far behind those of Japan., as well as the efforts in the combination of production, education and research and the commercialization of scientific research results. Combined with the national conditions in China, suggestions are put forward, including to strengthen the top-level design of scientific instruments, increase funding, promote the research and development of key core technologies, optimize the project evaluation system, promote industry-university-research cooperation, and the transformation of scientific and technological achievements to promote the high-quality development of advanced scientific instruments in China.