In people’s daily life, egg is one of the main animal protein foods, which will produce different emissions on its breeding procedure. Therefore, in order to promote the development of China’s layer industry, it is necessary to reduce pollutant emissions by improving efficiency. This paper uses Minimum distance to weak efficient frontier-Metafrontier Malmquist Luenberger (MinDW-MML) index model, by considering environmental factors and scale heterogeneity, to explore the evolution characteristics of laying hens breeding green total factor productivity (LHG) in China based on the data of 24 major laying provinces (municipalities) from 2004 to 2018. The results show that: (1) From 2004 to 2018, medium-scale LHG in China is the highest, the small-scale is the second, and the large-scale is the lowest. In the light of regional distribution, the western region is the highest, followed by the central region, and the eastern region is the lowest. (2) From 2004 to 2018, the overall China’s LHG showed a positive growth, and the decomposition indicators were characterized by decreased efficiency and technological progress. In general, the layer industry is vulnerable and easily affected by external factors. (3) Results from common frontiers and group frontiers exist some differences. The LHG under the common frontier is lower than the LHG under the group frontier. Finally, according to the above empirical results, this paper puts forward policy suggestions to improve LHG and environmental protection suggestions for laying hens.