This paper constructs an input-output index system to measure the input-output efficiency of medical and health institutions in 31 provinces and cities in China from 2017 to 2021 by using three-stage DEA method, and provides policy reference for improving their efficiency. The results show that the input-output efficiency of medical and health institutions in China is relatively high, but there is still room for improvement. After adjustment, the average comprehensive technical efficiency of the east, central and western regions is ranked as middle > East > West. The per capita GDP and the proportion of government health expenditure in financial expenditure have a significant positive impact on the input-output efficiency of medical and health institutions in China, while the population density has a significant negative impact. External environment and random interference have significant influence on input-output efficiency of medical institutions. The development of input-output efficiency of medical and health institutions is uneven, and different efficiency improvement strategies should be formulated according to the actual situation of different places.