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The industrial revolution has brought a leap in productivity; however, some severe ecological environment and resource problems are coming out with the development of industrialization. To achieve sustainable development of social economy, green technology innovation emerges in response to the proper time and conditions. In this context, the correct approach to measure the efficiency of green technology innovation in China's industrial enterprises is an important research topic. Based on existing studies, this paper divides innovation activities into two stages based on the innovation value chain and constructs a two-stage evaluation index system including all kinds of undesirable outputs transferred from negative externalities of the ecological environment. To evaluate green technology innovation efficiency, SBM and EBM network DEA models are applied to conduct empirical analysis from the perspective of time and space. This paper also calculates the efficiency values based on the SBM model and the EBM model, respectively, and compares the differences between them. The results show that the efficiency value of the achievement transformation stage is significantly higher than that of technology development stage; there are noticeable gaps in the efficiency of green technology innovation between different regions of China. Besides, the eastern region has a better performance in green technology innovation than the western region and Qinghai has the best green technology innovation performance. Combining the empirical results, the corresponding policy recommendations are put forward. [ABSTRACT FROM AUTHOR]