With the increasingly severe environmental situation, incorporating environmental effects into the research framework of enterprise technology innovation efficiency, a two-stage DEA model was used to measure the green technology innovation efficiency of industrial enterprises in 16 prefecture-level cities in Anhui Province from 2018 to 2020, and the influencing factors were analyzed in combination with the Tobit model. The results show that the innovation efficiency in the R&D stage is significantly higher than that in the technology transfer stage, and the efficiency performance in the Wanjiang region is significantly better than that in the non-Wanjiang region. Government support, innovation atmosphere, and regional economic development level all have a significant positive impact on the efficiency value of the R&D stage of enterprises. Applied research and government support have a significant negative impact on the innovation efficiency value of the green technology conversion stage, and talent factors have a significant positive impact on this stage. In order to further improve the green technology innovation efficiency of industrial enterprises in Anhui Province, environmental protection should be taken into consideration, an evaluation index system for green technology innovation efficiency of industrial enterprises should be established, and a green economic development model should be established.