Scientific and technological innovation ability is the supporting force for the implementation of national strategy. As the internal driving force of technological innovation, high-tech enterprises are of great significance to national development. On the premise of time lag effect, the dynamic Two-stage DEA model is applied to divide innovation activities into two stages: technology R & D and achievement transformation, and a two-stage innovation input-output index system is built to measure the technological innovation efficiency of high-tech enterprises in 19 sub provincial and above cities in China from 2016 to 2019.The results shows that there are striking contrasts in the technological innovation efficiency of high-tech enterprises between 19 sub-provincial and above cities, and the overall efficiency is low. Moreover, most cities pay more attention to technological R & D rather than the transformation of technological achievements. The R & D stage mainly depends on economies of scale, the contribution rate of pure technical efficiency in the transformation stage is relatively high, and the innovation efficiency of most enterprises needs to be improved. The results could provide a new perspective for the technological innovation activities of high-tech enterprises in different regions.