Traceability system is an important means to ensure food safety in China and consumers’ willingness to pay (WTP) for traceable food products is of great significance to improve the traceability system. Based on a consumer survey data in Beijing, Shanghai and Jinan, and applying a Logit model, this paper seeks to measure consumers’ WTP for the traceable beef, bean sprouts and lettuce and to explore its influencing factors. In addition, this paper also analyzes the heterogeneity of consumers’ WTP in different regions and products. Results show that consumers generally understand the traceability system, but their cognitive depth needs to be further improved. Consumers are willing to pay extra for traceable food products. According to regression results, consumers are willing to pay for traceable bean sprouts, lettuce and beef with 7.341 yuan/kg, 7.941 yuan/kg and 19.139 yuan/kg, respectively, which are generally higher than those of foreign countries. Influencing factors of WTP for different products are different. Among them, product price, place of purchase, risk perception, health status and income level are common driving factors. There is no significant difference in willingness to pay among different regions, which is consistent with the overall results. Therefore, business should reasonably classify pricing, gradually expand the traceability market, deepen consumer awareness, increase their risk perception, and improve the traceability system with the participation of multiple entities.