Various food safety and environmental problems in China have raised consumer awareness of food safety issues and negative environmental impacts in various supply chains. This research assessed consumer preferences and willingness to pay (WTP) for food safety and ecosystem delivery attributes associated with apples, demonstrated through the application of different traceability systems. Research participants were recruited in Beijing (N = 384) and Shanghai (N = 320). Choice experiment methodology was applied. The data were analyzed using conditional logit, random parameter logit, and latent class models; the results indicated significant consumer preferences for traceability information, including in relation to lower pesticide usage and application of organic fertilizer during primary production. The results also indicated that participants in this research had a significant willingness-to-pay premium for apple products that had production information traceability, had reduced pesticide use, and were grown with organic fertilizers. The models demonstrated heterogeneous preferences among participants such that consumers could be divided into three classes: non-price-sensitive (53.5%), pesticide-sensitive (21.7%), and price-sensitive (24.8%).