Agricultural greenhouse gas (GHG) emissions are influenced by a combination of climate, soil and agricultural management practices. Over the past 30 years, approximately 5% of China's cropland has shifted from the south to the north. This shift has significantly altered the geographical environment, with potential substantial impacts on agricultural GHG emissions. This study used the DeNitrification DeComposition (DNDC) process-based model to simulate GHG emissions (CH4 and N2O) from the production of China's 10 major food crops and explored changes in agricultural GHG emissions caused by the spatial shift of cropland in China. Results from the validated DNDC model indicate that total emissions from the major food crop production in China were approximately 343 Tg CO2-eq yr-1 with CH4 emissions accounting for about 74%. Meanwhile, the spatial shift of cropland from 1990 to 2020 resulted in a 3% decrease in average CH4 emissions per unit cropland area and an 8% increase in average N2O emissions per unit cropland area, respectively. The expansion of dryland in the Northwest Arid Region emitted less CH4 but significantly more N2O, thereby driving changes in national GHG emissions. This study provides a scientific foundation for the sustainable use of cropland and the formulation of strategies to reduce agricultural GHG emissions.