Green technology innovation is an important means to break out of the constraints of resources and the environment, enhance the competitiveness of enterprises, and achieve the upgrading of industrial structures, and promote high-quality economic growth. In order to realize the overall improvement of the green technology innovation capability of Chinese enterprises, it is necessary to measure the efficiency of industrial enterprises’ green technology innovation and explore their regional differences. In this paper, from the perspective of a two-stage innovation value chain, by introducing the industrial carbon emissions per unit of Gross Domestic Product (GDP) and the “three wastes” pollutants into the research framework of green technology innovation efficiency, we established a novel green innovation efficiency evaluation indicator system for industrial enterprises. Furthermore, we used a two-stage network DEA with shared input to measure the efficiency of regional enterprises’ green technology innovation and explored the regional differences in industrial enterprises’ green technology R&D and the efficiency of green technology achievement transformation. Finally, we provide some suggestions for improving China’s industrial enterprises’ green innovation efficiency, so that they can ameliorate the significant regional imbalances and differences and realize high-quality economic growth.
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