Food safety problem happens frequently in recent years, it is necessary to pre-warning the food safety risk, therefore the set-valued statistics model is applied in it. Firstly, research progress of food safety pre-warning system at home and abroad is summarized. Secondly, the theory model of set-valued Statistics is studied; thirdly, the structure of food safety risk pre-warning system is designed; then the corresponding pre-warning analysis steps of food safety risk based on set-valued statistics. Finally, the application of set-valued statistics model on food safety pre-warning is carried out, results show that the set-valued statistics method is an effective for analyzing the food safety problem.