Objective To explore the resource allocation efficiency and its influencing factors of traditional Chinese medicine hospitals in 30 provinces during the 13th five-year plan period. Methods Based on the data of China Health Statistical Yearbook and China Statistical Yearbook from 2016 to 2020, the BCC model was established to calculate the average value of resource allocation efficiency of TCM hospitals in China during the past 5 years, using Tobit model of panel data, the proposed hypothesis is verified and the factors affecting efficiency are found. Results During the period of “Fifteen”, the resource allocation of TCM hospitals in 30 provinces was DEA effective in 4, weak effective in 6, and ineffective in 20. The doctor allocation density and the ratio of medical and nursing administrators have significant negative and positive effects on the overall efficiency of resource allocation in TCM hospitals The spatial distribution density and the level of competition between TCM and western medicine have significant negative and positive effects on the scale efficiency of resource allocation in TCM hospitals, respectively. Conclusion During the period of “Fifteen”, the resource allocation efficiency of TCM hospitals in most provinces of China should be improved, the existing resources should be allocated as a whole, the level of medical technology should be raised, and the personnel structure should be set up reasonably, we should establish a flexible incentive mechanism, attach equal importance to both Chinese and Western medicine, and give prominence to the characteristics of Chinese medicine.