By selecting 5 three-level indexes as evaluation indexes of Chinese medicine’s scientific innovation ability，using Delphi method to carry out multi-round expert consultation，to determine the weight of indexes at all levels，to calculate the score of Chinese medicine’s scientific innovation index，and to analyze the regional differences and reasons of Chinese medicine’s scientific innovation ability. This paper analyzes the current situation of scientific research and development of TCM from the aspects of funds，personnel，subjects，papers and patents. Some of these regions，especially those with developed economy and high scientific research level，attach great importance to the scientific research and innovation of TCM，and there is still great room for progress in the scientific research and innovation of TCM in areas with backward economy and low scientific research level. The present report argues that there are short-board problems in the field of scientific research and innovation of traditional Chinese medicine in China. Local administrative departments should draw lessons from other regional experiences on the basis of local advantages and formulate appropriate development plans to further promote the benign development of the field of scientific research and innovation of traditional Chinese medicine.