This paper constructs an index system to measure the input-output efficiency of healthcare institutions in 31 provinces of China from 2017 to 2021 by adopting the three-stage DEA method，and provides policy reference for improving their efficiency. The results show that the input-output efficiency of healthcare institutions in China is relatively high as a whole，but there is still room for improvement. The ranking of the adjusted mean values of comprehensive technical efficiency in the east，central and western regions are Central ＞ East ＞ West. The per capita GDP and the proportion of general government health expenditure in financial expenditure have a significant positive impact on the input -output efficiency of healthcare institutions in China，while the population density has a significant negative impact. External environment and random interference significantly influence the input-output efficiency of medical institutions. The development of input- output efficiency of healthcare institutions is uneven. Therefore，we recommend formulating different efficiency improvement strategies according to the actual situation of each place.