The high-tech enterprise, which is knowledge-intensive and technology-intensive, is not only a necessary element to promote the development of economy and society, but also plays an important role in national development. According to the characteristics of technological innovation of high-tech enterprises as well as the time lag effect, we construct the two-stage input-output index system of technological innovation of high-tech enterprises. Then we evaluate the two-stage performance by using the two-stage DEA model. Through the evaluation of the technological innovation performance of high-tech enterprises in 27 regions of China from 2012 to 2015, this paper comprehensively analyzes the efficiency of the high-tech enterprises in the technology research stage and technology transform stage. It is found that from the perspective of technological innovation level, there is a big gap among the high-tech enterprises in our country. Moreover, the high-tech enterprises in most areas tend to focus on the intermediate achievements and ignore the commercialization of production. Therefore, aimed at the differences of technological innovation of enterprises in different regions, we need to put forward more targeted measures. The research results provide a tool for a more objective evaluation of the technological innovation level of high-tech enterprises in different regions in China. Meanwhile, they also provide a decision-making basis for formulating the corresponding high-tech enterprise technological innovation policies.