Abstract: Studies on the country’s food system and greenhouse gas (GHG) accounting are still lacking in China. Most of previous studies have focused on crop and livestock production, which are hard to meet the demands of both GHG reduction and sequestration, against the backdrop of the “carbon peak and neutrality” policy. In this study, we proposed a food system GHG accounting framework that covers land use, land use change, and forests (LULUCF); agricultural production; and post-production food supply sectors. Through literatures review, collecting emission data, and reverse-calculating emission factors, we analyzed the differences in accounting methods and the uncertainties of emission parameters for various GHG emission (or sequestration) segments in the Chinese food system. Results showed that the coefficients of variables (CVs) of the emission or storage parameters of manure and crop straw application, pesticides and film production, food processing, food retail and wholesale, and grassland sinks were above 35%. Our suggestions for future studies are as follows: 1) in the agricultural production sector: refine emission factors of agricultural activities, harmonize different energy use accounting methods (e.g., final energy consumption accounting and process-based accounting methods), and reinforce research on energy consumption of agricultural input manufacturing enterprises; 2) in the LULUCF sector: establish the land use classification dedicated to global change research, identify the land use processes associated with the food system, and cross-check the field measure-based accounting method and the process-based accounting method; 3) in the post-production food supply sector: clarify the accounting scopes of each stage and select the environmental input-output life cycle assessment method, the process-based life cycle assessment method, or the final energy consumption accounting method. This study could further provide scientific basis for GHG reduction in food systems.