Background: As the core of the county-level Maternal and Child Health Hospitals (MCHH) in rural areas of China, the service efficiency affects the fairness and availability of healthcare services. This study aims to identify the determinants of hospital efficiency and explore how to improve the performance of MCHH in terms of productivity and efficiency., Methods: Data was collected from a sample of 32 county-level MCHHs of Guangxi in 2014. Firstly, we specified and measured the indicators of the inputs and outputs which represent hospital resources expended and its profiles respectively. Then we estimated the efficiency scores using Data Envelopment Analysis (DEA) for each hospital. Efficiency scores were decomposed into technical, scale and congestion components, and the potential output increases and/or input reductions were also estimated in this model, which would make relatively inefficient hospitals more efficient. In the second stage, the estimated efficiency scores are regressed against hospital external and internal environment factors using a Tobit model. We used DEAP (V2.1) and R for data analysis., Results: The average scores of technical efficiency, net technical efficiency (managerial efficiency) and scale efficiency of the hospitals were 0.875, 0.922 and 0.945, respectively. Half of the hospitals were efficient, and 9.4 % and 40.6 % were weakly efficient and inefficient, respectively. Among the low-productiveness hospitals, 61.1 % came from poor counties (Poor counties in this article are in the list of key poverty-stricken counties at the national level, published by The State Council Leading Group Office of Poverty Alleviation and Development, 2012). The total input indicated that redundant medical resources in poverty areas were significantly higher than those in non-poverty areas. The Tobit regression model showed that the technical efficiency was proportional to the total annual incomes, the number of discharge patients, and the number of outpatient and emergency visits, while it was inversely proportional to total expenditure and the actual number of open beds. Technical efficiency was not associated with number of health care workers., Conclusion: The overall operational efficiency of the county-level MCHHs in Guangxi was low and needs to be improved. Regional economic differences affect the performances of hospitals. Health administrations should adjust and optimize the resource investments for the different areas. For the hospitals in poverty areas, policy-makers should not only consider the hardware facilities investment, but also the introduction of advanced techniques and high-level medical personnel to improve their technical efficiency.