Food systems, including supply chains, account for approximately one-third of global anthropogenic GHGs emissions. We construct a bottom-up GHG inventory of China’s food system from farm to fork for the period 1990–2018. The decomposition method is used to assess regional differentiated drivers. GHG emissions reduced by 6.8% between 1990 and 2000 due to energy structure changes in East, Central and Southwest China. They then increased by 2.3% (2001–2010) because of rapid economic growth. Further large increases of 13.1% (2011–2018) were driven by growing consumption expenditure and GHG-intensive food consumption. In 2018 total emissions from China’s food system, including supply chains, was 1.55 Gt CO2e yr-1 (95%CI 1.07-2.03 Gt CO2e yr−1). Scenario simulation shows that demand- and supply-side synergies can offset emissions increases from high-quality protein food demands. Results demonstrate the importance of supply-side production spatial optimization and green source food importation for mitigating GHGs emissions.