This study aims to construct a binary logit model which considers consumer acceptance and choice behavior in Taiwan when they consume foods with the food traceability. Based on the prior literatures on food traceability, most of them focused on the contributions of food traceability for companies, the benefits for food chains, or the price that consumers are willing to pay. There are few literatures putting their emphases on the demand aspects. Moreover, the binary logit model implies that all of decision makers are as homogeneous which is a drawback. Therefore, this study discussed the factors which are associated with consumer acceptance of foods with food traceability from the demand perspective. Moreover, this study changed to adopt interaction between variables in the binary logit model to represent the heterogeneity of decision makers. This study used the stated preference method to develop the questionnaire to explore the consumers’ basic knowledge of food traceability, the concern level of food safety, food hygiene, and personal health. Furthermore, this study also took the price, personal lifestyle and socio-economic variables as the factors which have impact on consumers’ choice behavior. Based on samples which are classified by the types of foods, this study explored the impact of different types of foods on consumer choice of foods with food traceability. In addition, this study also considered the price effects on different groups of consumers. The results indicated that the major factor which affects consumers’ choice behavior is the price of foods with food traceability. The less important factor is concern level and basic knowledge for foods. Moreover, the price of foods affects the probability of heterogeneity consumers to choose foods with food traceability. For those people who have higher incomes, the results present the positive effects. Furthermore, general consumers prefer to choose foods with food traceability when these products have short storage life and require refrigeration.