Objective: To analyze the operational efficiency of traditional Chinese medicine hospitals in poverty-stricken counties in 2019, in order to provide decision-making basis for preventing the return to poverty due to illness and consolidating the achieve- ments of poverty alleviation. Methods: Taking 611 Chinese medicine hospitals in poverty alleviation counties in 22 provinces of Chi- na as the research object, the three-stage data envelopment analysis model was used for analysis. Results: After using the three-stage data envelopment analysis model, the comprehensive efficiency value of the Chinese medicine hospitals in poverty alleviation county was 0.952, the technical efficiency value was 0.988, and the scale efficiency value was 0.962. Compared with before adjustment, the main reason for the low efficiency of hospital operation was the low efficiency of scale. Conclusion: After removing environmental vari- ables and random confounding, the real level of operating efficiency of TCM hospitals in poverty alleviation counties has improved compared with that before adjustment, that is, the operating efficiency of hospitals is vulnerable to external factors, and the real level is easy to be underestimated. For the development of traditional Chinese medicine hospitals in poverty-stricken counties, it is necessary to continuously increase economic investment, while paying attention to the construction of hospital connotation, effectively reducing external interference, and effectively leveraging the true level of the hospital.