Consumer preference for the mandatory labeling of genetically modified (GM) foods promotes public support for the implementation of GM food policies. This study analyzes consumers’ preference for the traceability of GM soybean oil. Survey data were collected through a self-administered survey covering 804 randomly sampled urban residents in the eastern, central and western regions of China. Using a logit model, this analysis examines the impacts of influential factors on consumers’ preference for traceability. The results show that about 56.5% of the respondents have a positive preference for the traceability of GM soybean oil. Factors increasing the preference for traceability include a better perception of the attributes of nutrition benefit and potential health risk, perceived inadequacy of simple mandatory labels, more attention paid to food labels, and distrust in the agencies overseeing GM food safety. Enhancing consumers’ perceptions of GM-related attributes and awareness of food labels will help improve the mandatory labeling management of GM foods.