China's rapid urbanization is transforming its food system, encompassing agricultural production, processing, distribution, retail, and consumption, with profound implications for greenhouse gas emissions. Using a comprehensive assessment framework, we quantified China's food-system greenhouse gas emissions from 2000 to 2019, a period characterized by accelerated urbanization. National food-system emissions increased from 1.63 to 2.14 gigatons of CO2-equivalent, driven largely by energy-intensive food processing and transportation. While agricultural production remained the largest source of emissions, the relative contribution of post-production stages increased from 33.6% to 48.3% as urbanization advanced. There are striking disparities among provinces. In highly urbanized municipalities, post-production stages accounted for more than 70% of food-system emissions, whereas in low-urbanization provinces they accounted for under 30%. These findings reveal the structural linkage between urbanization and food-system emissions, providing critical insights for developing targeted low-carbon food strategies and advancing sustainable urban development.