Long-Term Annual Changes in Agricultural Carbon Footprints and Associated Driving Factors in China from 2000 to 2020

China is one of the world’s largest agricultural producers, and its agricultural carbon footprint (CF) is a major contributor to global warming. However, the long-term annual changes in its agricultural CF and the underlying driving factors remain largely unknown, compromising the scientific basis for effective carbon reduction and sustainable agriculture management. To this end, we used the life cycle assessment (LCA) method and statistical data to calculate long-term annual agricultural CFs in China. We then adopted the linear regression slope and the Moran’s I method to analyze the temporal trends and spatial clustering characteristics and revealed the correlations between the main drivers and agricultural CFs. The results showed that the total (TCF) and farmland-averaged carbon footprint (FCF) of crop production both increased first and then decreased in China from 2000 to 2020, with a turning point in 2015. Overall, the TCF increased by 6.82% (3022.16 × 104 t CO2 eq), while the FCF slightly decreased by 0.004% (0.01 t CO2 eq/ha). Both the TCF and the FCF showed spatial heterogeneity, with high values in the east and low values in the west, and the spatial clustering of the TCF and its components has weakened over time. Fertilizer (39.26%) and paddy (27.38%) were the main contributors to TCF. Driver analysis found that grain yield was positively correlated with TCF in most provinces, indicating that the continuous yield increase has brought greater pressure on agricultural carbon emission reduction in China. Agricultural stakeholders should optimize crop planting structures and patterns and improve resource-use efficiencies through technological and management innovation to adapt to these threats and achieve low-carbon agriculture. The findings of our research can aid the scientific research on spatiotemporal estimation and driver analysis of agricultural CFs and provide decision-making support for sustainable agricultural practices.