Tracing the spatial transfer and heterogeneity of agricultural methane (CH4) and nitrous oxide (N2O) emissions in China is a prerequisite for the sustainable transformation of agricultural systems. In this study, we established a research framework for evaluating agricultural CH4 and N2O flows and convergence. Using this framework, we established an inventory of China's agricultural CH4 and N2O emissions calculated according to the IPCC inventory guidelines, built a food trade model to simulate the spatial transfer, and revealed the regional differences. Finally, we analyzed the influence mechanism by combining extended Kaya identity and the logarithmic mean divisia index (LMDI) model. We found that inter-regional transfer of agricultural CH4 and N2O emissions in China have intensified, increasing from 56.14 % of total transfers in 2000 to 67.28 % in 2019. The spatial inequalities of agricultural CH4 and N2O increased, and emission intensity varied more within regions than between regions, with per capita emissions showing a club convergence with “intragroup convergence and intergroup divergence”. Although the contribution of agricultural CH4 and N2O emissions varies across provinces, controlling emissions intensity and land use intensity while maintaining GDP per capita is the key to emission mitigation. Our study provides theoretical support for prioritizing policies to mitigate agricultural CH4 and N2O emissions.