We investigated 12 county-level public hospitals in eastern, central and western China respectively. The questionnaires were used to investigate the operation of hospitals. Data envelopment analysis was conducted on the surveyed data. The Tobit regression model was used to analyze the influencing factors. The overall efficiency of the 36 hospitals was 0.889, and the quantity of the overall efficiency, pure technical efficiency and scale efficiency reched 1 as 14 (38.89%), 18 (50.00%) and 14 (38.89%) respectively. The scale of returns is increasing, diminishing, constant as 13 (36.11%), 9 (25.00%) and 14 (38.89%) respectively. The results of regression analysis showed that both the outpatient and emergency visits per capita and the number of beds actually opened were positively correlated with the overall technical efficiency of hospitals, and the per capita fixed assets were negatively correlated with them. The per capita physician emergency department volume, the actual number of open beds and purely technical efficiency was positively correlated, while the proportion of total income of drugs and its negative correlation. The overall efficiency of sample hospitals needs to be improved. Some hospitals should pay attention to the negative impact of over-expansion, plan the number of beds rationally, the use of existing assets and the workload of doctors, improve the medical technology and value, and realize the development of hospitals depending on medical technology, not drug revenue.