Objective To evaluate the efficiency of basic public health services of districts and counties in Chongqing in 2014 and provide reference for project implementation in the future. Methods The data envelopment analysis (DEA) was used to evaluate the comprehensive efficiency, pure technical efficiency, and scale efficiency for all districts and counties in Chongqing. Results The average comprehensive efficiency, average pure technical efficiency, and average scale efficiency of basic public health services in Chongqing in 2014 were 0.800, 0.890, and 0.899, respectively. Fifteen districts had valid DEA results and 20 districts had invalid DEA results. Of these 20 districts, 11 districts had progressively declined scale efficiency and 9 districts had progressively increased scale efficiency. Conclusion The efficiency of basic public health services in Chongqing needs to be improved. The development across functional districts is unbalanced. The flexibility of fund distribution and the flow of talent should be reinforced and the efficiency of resource utilization and output indexes need to be improved.