Based on the agricultural new quality productivity index and agricultural carbon emission efficiency of provincial administrative regions in China from 2012 to 2021, this study empirically examines the impact of agricultural new quality productivity on agricultural carbon emission efficiency. Furthermore, it examines the mediating role of agricultural industrial structure upgrading, as well as the moderating effect of industrial diversification. The key findings can be summarized as follows: (1) The baseline regression shows that agricultural new quality productivity can significantly improve the development of agricultural carbon emission efficiency. This conclusion remains robust after considering endogeneity and after a series of robustness tests; (2) The mediating effect analysis reveals that agricultural new quality productivity enhances agricultural carbon emission efficiency by facilitating the upgrading of the agricultural industrial structure; (3) The moderating effect analysis demonstrates that industrial diversification significantly and positively amplifies the impact of agricultural new quality productivity on carbon emission efficiency; (4) Heterogeneity analysis indicates that the effect of new quality productivity is more pronounced in eastern provinces and markets with high maturity.