Abstract: Clearing the fast track connecting scientific research and industrialization, and promoting the accurate connection between the innovation chain and the industrial chain are important ways to achieve scientific and technological self-reliance and high-quality economic development. Taking the projects of National Natural Science Foundation of China as an example, to better play its mission of scientific and technological revolution in the new era in promoting basic research, application research and important innovation, and strengthen the supporting effect of scientific and technological innovation on economic development from the innovation chain source effectively, after a questionnaire survey of 126 experts from the Department of Engineering and Materials Science of the Natural Science Foundation of China, through a combination of quantitative and qualitative analysis of the data, a linking mechanism of scientific problem formation and scientific achievement transformation from the perspective of the whole process is proposed and conducted. The study analyzes the whole process of management, from scientific problem formation, scientific projects evaluation, scientific research achievement output and application mechanism, the whole process of the interaction mechanism cycle between the forward formation and reverse formation of scientific problems, and the whole process effect of scientific research paradigm transformation and interdisciplinary integration, and the feasibility of the linking mechanism is verified by case study. Consequently, the study puts forward the strategies and suggestions to ensure the efficient operation of the linking mechanism for the scientific problem formation and scientific achievement transformation in the perspective of the whole process.