This paper, taking organic tomato for example, uses BDM mechanism auction experiment to study consumer’s preferences of food safety certification labels and then it analyzes the related influencing factors with the help of multivariate Probit model.The result shows that consumers’ bid for tomatoes with EU organic certified label is much higher than those with Chinese organic certified labels, but it has no obvious difference with the bid for tomatoes labeled with both kinds of labels. For consumers with different personal features, their preferences for certification labels are different. Consumer’s food safety awareness and knowledge of organic have positive influence on their willingness to pay, while the influence of environmental awareness on consumer’s preferences for certification label is not significant. Therefore, this paper proposes that government certification system arrangement and strategic decisions of the manufacturers should give full consideration to consumer preferences of different certification label so as to meet the diverse market demands.