The National Natural Science Foundation of China（NNSFC） is an important index to measure the innovation research ability of the institute. To provide decision and basis for improving Traditional Chinese Medicine（TCM） research ability and management level， this study started with the projects funded by NNSFC， analyzed the applicant’s gender， age， educational background， professional title， and the categories and guide codes of the declared projects， analyzed the situation of obtaining NNSFC project funding from 2009 to 2018，summarizedthe effectiveness， experience and shortage of scientific research management. Through analysis， it is found that loose research system， unbalanced disciplines development and insufficient efforts to organize declaration are the key problems that make it difficult to steadily improve the success rate of funded projects from NNSFC. In order to improve the scientific research capacity of TCM， it is necessary to improve the project declaration and management model， promote the cross-integration of disciplines， and focus on training young talents.