This study offers a RAGA-PP-SFA model to measure green technology’s innovation efficiency in the high-end manufacturing industry. The study’s aim is to solve the shortcomings of traditional SFA methods that are unable to improve multi-output efficiency. The RAGA-PP-SFA model presented here is based on the multi-emission and multi-output characteristics of high-end manufacturing innovation activities. Using panel data from 2010 to 2015 on China's high-end manufacturing industry and considering factors such as environmental regulation, government subsidy, and market maturity, this paper empirically examines and compares the efficiency of green technology innovation versus traditional technology innovation, as well as regional heterogeneity in China's high-end manufacturing industry. The study ultimately found a low level of green technology innovation efficiency in China’s high-end manufacturing industry. However, an overall rising trend shows that the green development of China's high-end manufacturing industry has achieved remarkable results. Green technology innovation efficiency in high-end manufacturing industries across various regions was generally lower than the efficiency of traditional technology innovation. Both types of efficiency showed a pattern of “high in the east and low in the middle and in the west”. High-high efficiency is primarily found in the east, whereas the west is characterized by low-low efficiency. There are significant differences between regions, pointing to an equal rate of development. Government subsidies and enterprise scale had a significant negative impact on green technology innovation efficiency in regional high-end manufacturing industries, while market maturity and industrial agglomeration had a significant positive impact. Based on the study’s findings, environmental regulation and openness to the outside world play insignificant roles in green technology innovation efficiency.