Evidence of China’s food loss and waste (FLW) and its increasing impacts on food security and environmental sustainability is urgently needed to guide policy intervention and avoid unnecessary damage to human health and the environment. This paper estimates the scale of China’s FLW in 2019 and assesses the environmental impacts of major food types along the entire food supply chain (FSC) by using a food balance and material flow analysis (MFA) based on existing empirical research. The results show a total FLW of 422.56 Mt which is around 22.37% of total food production (1889.12 Mt). There are also serious environmental impacts on the land footprint (LF), water footprint (WF), and the carbon footprint (CF) estimation (4152.36 × 109 gm2, 613.84 × 106 t CO2e and 506.07 × 109 m3 on average, respectively), most of which are found in foods of animal products, cereals, vegetables and fruit at the stages of consumption, agricultural production, postharvest handling and storage. In addition, the root causes of FLW generation at different levels—micro, meso and macro—were also analyzed. These results will provide significant guidance to researchers and decision-makers on primary data collection and reduction-policy development for China’s FLW.