The decision in 2006 to abolish the agricultural tax, which had lasted for thousands of years, contributed to the prosperity of agriculture, and with it the growing importance of soil N2O emissions in China. However, most of the previous literature ignored soil N2O emissions due to their too small share in total agricultural greenhouse gas (GHG) emissions. This paper attempts to take soil N2O emissions as an important variable in the measurement of agricultural green total factor productivity (AGTFP), which incorporates environmental pollution into the analytical framework of agricultural production efficiency. Three impressive results were found. Firstly, soil N2O emissions play an increasingly important role in agricultural GHG emissions. The proportion of soil N2O emissions in agricultural GHG emissions increased from 4.52% in 1998 to 4.83% in 2006, and then to 5.36% in 2016. Secondly, the regional difference of soil N2O emissions in AGTFP is visible. In 2016, although soil N2O emissions accounted for a small proportion (about 5%) of the total agricultural GHG emissions in China, the AGTFP including soil N2O emissions was much lower than that excluding soil N2O emissions, especially in areas with high agricultural and population density. Finally, over time, soil N2O emissions have had an increasing effect on AGTFP. Compared with 1998–2006, the impact of excluding soil N2O emissions on AGTFP in 2007–2016 was more evident than that including soil N2O emissions.
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