Based on the regional panel data of 2011-2018, this investigation firstly employs three-stage Malmquist index to evaluate the green innovation efficiency of Eight Comprehensive Economic Areas in China. Then, according to the different causes of low technology efficiency in different areas, Eight Comprehensive Economic Areas are classified into four categories utilizing pure technology efficiency and scale efficiency matrix. Additionally, the comparison between original and revised Malmquist index is illustrated. The empirical findings are as follows: (1) The green innovation efficiency in the whole country is on the rise. South coast, Northwest and Southwest are ahead of the country. (2) Accelerating the development of technology market and optimizing the industrial structure contribute to the advancement of green innovation efficiency. (3) The green innovation efficiency in the first stage is overestimated due to the overestimated technical efficiency. Furthermore, the fundamental reason for low technical efficiency is low scale efficiency. (4) After excluding the interference of external environment and random factors, the Malmquist index of each region declines. Additionally, the national average value of green innovation efficiency descends from 1.105 to 1.047, and Northwest and Middle Yellow River decreases 5 ranks and increases 3 ranks, respectively.