The data envelopment analysis (DEA) is used to measure the comprehensive efficiency, pure technical efficiency and scale efficiency of scientific and technologicalinnovation of prefecture-level cities in Hunan Province from 2015 to 2019.Tobit model isestablished to analyze the main influencing factors of scientific and technological innovation efficiency.The results of research shows that the overall level of scientific and technological innovation efficiency of prefecture-level cities in Hunan province increased from 2015 to 2019, but there is a big gap among cities, and the comprehensive efficiency and pure technical efficiency are lower.Regional economic development level, scientific research personnel, government support and industrial structure have a significant impact on scientific and technological innovation efficiency. On the basis of this, in order to improve the efficiency of scientific and technological innovation of Hunan province, reasonable allocation of economic resources, introduction and cultivation of high-level scientific and technological talents and active development of high-tech tertiary industry are put forward.