In response to increasing concerns about domestic food safety issues, establishing tracking systems in the food industry is mandatorily required under newly launched food safety laws. However, the kinds of monitoring and certification systems that should be set up to ensure practical adoption and the effectiveness of the regulation remain unclear. This study aims to analyze consumers’ preferences for milk traceability, with particular interest in investigating how consumers’ preferences could be affected by monitoring and certification systems of the regarding system. Survey data from a choice-based conjoint (CBC) experiment are used to achieve this objective. In the experiment, milk is defined by a set of attributes in which we assume that milk traceability can be certified by three entities: the government, an industrial association, and a third party. The CBC data are then analyzed by using the alternative-specific form of a conditional Logit (McFadden's Choice) model. We found that urban Chinese consumers have a strong desire for traceable milk, but their preference for traceable milk is significantly related to the associated certificate issuers. Currently, the highest willingness-to-pay goes to government certificated traceable milk, followed by industrial association certificated and third-party certificated milks. In the future, however, consumers are likely to give more credit to third-party certification with rising income and knowledge.