The symposium on industrial green and low-carbon development held by the Ministry of Industry and Information Technology in January 2024 emphasized the need to steadily promote carbon reduction in the industrial sector, and improving the efficiency of green technology innovation in industrial enterprises has important practical significance in promoting their green transformation and upgrading. Therefore, this article uses inter-provincial panel data from 2005 to 2022, and constructs super efficiency EBM model, ML index model, Dagum Gini coefficient model, and spatial Durbin model to measure, decompose, analyze the sources of differences and influencing factors in the two-stage efficiency of industrial enterprises. The results show that the efficiency of technology research and development is higher than the efficiency of technology transformation, and the efficiency level of each stage is directly proportional to the economic development level of the region. The scale efficiency level of each stage remains stable at 0.9 or above, and the low pure efficiency is an important reason for the significantly low efficiency. The efficiency level of each stage shows an increasing trend from 2005 to 2022, and the efficiency level of each stage in the eastern region is higher than that of other regions. The efficiency level of China’s research and development stage shows a good development trend, but there is insufficient coordination between technological efficiency and technological progress in the transformation stage, and there are significant bottlenecks in the technological progress index. The differences in efficiency levels between different stages mainly come from the differences in efficiency levels between regions, with more significant differences between the eastern region and other regions. The industrial structure and market competitiveness have a significant promoting effect on efficiency levels, while environmental regulations have a significant inhibitory effect on efficiency levels.