The super-efficiency DEA model was used to measure the industrial innovation efficiency of the national new area without considering the undesired output and considering the undesired output，and further used the panel Tobit regression model to explore the factors affecting industrial innovation efficiency. The results of the study show that the industrial innovation efficiency of the national-level new zones in both cases shows a simultaneous change and decreases year by year；the industrial innovation efficiency of the new zones established later in the central and western regions is higher，while the economically developed eastern regions established earlier are lower；government support and finance Service has a significant positive impact on the industrial innovation efficiency of China’s new zones. Based on the empirical research conclusions，and drawing on the experience of other national-level new area developments，it proposes specific countermeasures and suggestions for the industrial development of Xiong’an New Area.