Food systems are responsible for a third of global anthropogenic greenhouse gas emissions and there has been an increasing research focus on food-system greenhouse gases. However, limited attention has been paid to emissions from the regional trade network associated with food systems. Here we developed a multi-regional input-output-based hybrid life cycle assessment model and traced China’s food-system greenhouse gas emissions from farm to fork. China’s food system emitted 2.4 (95%; confidence interval range: 1.6–3.2) gigatons CO₂-equivalent in 2019, and half were emitted at the production stage. There were substantial differences in the emission structure and sources among the provinces. Further analysis indicated that the differences among provinces were caused by the separation of food production and consumption. People living in wealthier coastal and central regions consumed food from western and northeastern regions. Therefore, the government should consider interregional synergies when developing strategies to reduce food-system greenhouse gas emissions.