BackgroundCounty-level public hospitals play an important role in China's medical tertiary health care network. Since a new round of medical reforms occurred in 2009, county-level public hospitals have conducted continuous exploration and reforms. To analyze the efficiency and productivity of 36 county-level public hospitals based three provinces in China.Methods.We randomly selected 12 county-level hospitals from each 3 provinces based on economic levels and regional differences in China, finally, a total of 36 county-level hospitals were chosen, and a self-made questionnaire was used to investigate hospital operations for collecting data from 2011 to 2015. 2011–2015 is the twelfth five-year period of China's national economic and social development. Four input indicators and three output indicators were selected. Data envelopment analysis and the Malmquist index methods were used to measure the efficiency and productivity by the key indicators for each region.Results.On average, four input indicators in three regions have continued to grow from 2011 to 2015. The output in the three regions is directly proportional to the upward trend in inputs. On average, the three output indicators of hospitals in the eastern region are higher than the central and western regions. The technical efficiency of county-level public hospitals in the central, eastern, and western regions of China were on an upward trend, and the number of the technical efficiency, the pure technical efficiency, and the scale efficiency values reaching 1 in the three regions was more than half, respectively. The average of total factor productivity change for 2011–2015 in the central, eastern, and western regions was 1.016, 0.997, and 0.930, respectively.Conclusions.The efficiency of the central Chinese region was mainly affected by pure technical efficiency; however, scale efficiency changed to affect the efficiency of the eastern and western hospitals in 2015. The increase in production efficiency in the central region was driven by the technical efficiency. In the future hospital management, management innovation needs to be strengthened. The decline in productivity in the eastern region was due to the decline in the technical efficiency. At present, the eastern region pays attention to management innovation, but it is necessary to be alert to the adverse consequences of the expansion of hospital scale. The decline in productivity in the western region was due to the decline in the technological efficiency and technical efficiency. The hospitals should strengthen hospital management and blind scale expansion. Financial subsidies in the western region have a significant role in promoting the development of hospitals. The internal management innovation of hospitals in the eastern region has a positive effect on the technical efficiency of hospitals. The medical reform measures in the central region have positively promoted the efficiency of hospitals.