Based on the panel data of Jiangsu National High-tech Zones from 2016 to 2020, the static and dynamic efficiency of Jiangsu National High-tech Zones was measured by data envelopment analysis（DEA） and Malmquist index, and the panel Tobit model was adopted to explore the reasons affecting the science and innovation efficiency of Jiangsu National High-tech Zones. The results show that the overall innovation efficiency of Jiangsu National High-tech Zones is not high, the scale efficiency is lower than the pure technical efficiency, and the technical factors play a major role.The total factor productivity is generally stable, and the technological progress index of most high-tech zones increases but the scale efficiency decreases. The degree of regional opening has a significant positive impact on the innovation efficiency of Jiangsu high-tech zones, and a significant negative impact on the intensity of R&D funds and the level of economic development. Therefore, it can be improved from the aspects of improving the utilization efficiency of innovative resources, improving the level of opening up to the outside world, optimizing the allocation of resources, etc., so as to effectively improve the science and innovation efficiency of Jiangsu National High-tech Zone.