Abstract: Two -dimensional code technology is an electronic tagging technology of combination of computer and optical technology. It is an important way for information collection and input. Two-dimensional code technology produced a series of safety problems. At the same time, it has been widely used in various fields of logistics, production automation,e-commerce. This paper improved the security of traditional two-dimensional code generation algorithm based on evolution encryption. This algorithm was applied to agricultural products quality and safety traceability system, and the results showed that improvements were effective.