ObjectiveThis article aimed to evaluate the efficiency trends and influencing factors of essential public health services in Hainan Province after the healthcare reform launched in 2009 in China.MethodsThe efficiency of essential public health services (EPHS) at primary health institutions was assessed using data envelopment analysis (DEA), and the efficiency change was analyzed by employing the Malmquist productivity index (MPI). We used Tobit regression to identify the influence of environmental factors on the efficiency of public health services. The bootstrap method was adopted to reduce the impact of random errors on the result.ResultsThe bootstrapping bias-corrected efficiency revealed that the average values of technical efficiency, pure technical efficiency, and scale efficiency were 0.7582, 0.8439, and 0.8997, respectively, which meant that the EPHS in Hainan Province were not at the most effective state. The average bias-corrected MPI was 1.0407 between 2010 and 2011 and 1.7404 between 2011 and 2012. MPIs were less than 1.0000 during other periods investigated, ranging from 0.8948 to 0.9714, indicating that the efficiency of EPHS has been decreasing since 2013. The Tobit regression showed that the regression coefficients of per capita GDP, population density, the proportion of older people aged over 65, and the proportion of ethnic minority population were 0.0286, −0.0003, −0.0316, and − 0.0041 respectively, which were statistically significant (p < 0.05).ConclusionThere was a short-term improvement in the efficiency of EPHS in Hainan after the launch of the new round of health reform. However, this trend has not been sustained after 2013. In particular, equalized financial investment in essential public health could not fulfill the needs of poor counties. This has resulted in the inability to improve scale efficiency in some counties, which in turn has affected the improvement of overall EPHS efficiency. Therefore, to promote EPHS efficiency sustainably, it is suggested that under this model of provincial control of counties, the equity of resource allocation should be effectively improved while further advancing the technology of service delivery.