Objective: To measure the input-output effect of the central transfer payment of traditional Chinese medicine (TCM) project funds and effectively improve the primary TCM service capacity. Methods: The non-radial SBM model was used to measure the efficiency of the central transfer payment funds in various provinces to improve the primary TCM service capacity. Results: In general, the efficiency of SBM model varies greatly among provinces, and economically developed areas are not better than underdeveloped areas. Based on regional analysis, the primary TCM service capacity performance o in the Pearl River Delta region is higher than that in the Yangtze River Delta region; the service capacity improvement performance of primary TCM in Anhui, Jiangxi and Hunan regions leads other central provinces in China; and the service capacity of primary TCM in the western region is steadily improving. Conclusion: It is needed to increase investment in primary TCM and continuously improve the primary TCM service capacity; implement the “TCM Talent Training Plan" to strengthen the primary TCM talent team; give full play to the role of performance evaluation, and guide provinces to attach importance to improving the primary TCM service capacity.