Since the 18th CPC National Congress, food safety issues have been highly valued by the Party Central Committee and the State Council and the situation of food safety has continued to improve in China. But the uncertainty of unknown food safety risks is still increasing. The outbreaks of the Novel Coronavirus Pneumonia happened nationwide in 2020 warned that we should strengthen ability of early identification and warning of major risks and develop mechanisms in food safety work. The present paper mainly studies the issues of institutional guarantees, operating mechanisms, and capacity building on food risk rapid identification and alert system. And some advice on strengthening this system are proposed.