With the continuous development and application of transgenic crops, more and more transgenic foods were launched on the market, and people paid more and more attention to the safety of these foods. While Chinas regulation of transgenic crops and products is not optimistic, and the organization level of production enterprise is low, if the domestic enterprises copy the foreign traceability system, the problems of unclose integration in production process management will appeared. Thus, combining with the existing production flow and situations of China’s transgenic crops enterprises and taking transgenic maize as example, a full traceability system model for transgenic crops and products was built based on the basic theory of workflow net, through the analysis of important steps which affect gene characteristics and quality security in genetically modified crops production process. Eventually, with the guidance of the model, a full traceability system model for transgenic crops and products was designed and developed, which showed great theoretical and practical significance.