Based on the panel data of 83 national high-tech zones from 2011 to 2018, the spatial differences and its influencing factors of innovation efficiency growth in national high-tech zones are investigated by utilizing the stochastic frontier model, K-R variance decomposition and panel data fixed effect model. The results show that:①the innovation efficiency of national high-tech zones shows a trend of first decreasing and then increasing, and the spatial differences are obvious, the innovation efficiency of eastern national high-tech zones growing fastest, followed by central national high-tech zones, and western national high-tech zones growing slowest.②the difference of scale efficiency is the main source of the difference of innovation efficiency growth in national high-tech zones; ③the level of economic development has a significant negative impact on the innovation efficiency growth of national high-tech zones, while human capital, industrial structure and internationalization have significant positive impacts on innovation efficiency growth. Based on the research conclusion, some suggestions are put forward to promote the collaborative improvement and balanced development of innovation efficiency of national high-tech zones.