A reasonable and effective special chemical management system can not only facilitate the application and use of chemicals by enterprises, but also facilitate the supervision of regulatory departments, and it can prevent special chemicals from flowing into illegal channels. In this paper, the design and implementation of special chemical management system is studied. A special chemical management system based on distributed workflow is designed. Symmetry and asymmetry XML encryption algorithms are combined together to ensure the information security of the system. This paper takes the special chemical management purchase process as an example to perform example analysis, and the study finally realizes the design of special chemical management purchase process, distributed circulation file and circulation file encryption based on XML encryption principle. The XML document encryption strategy proposed in this study can effectively ensure the safety of information related to special chemicals, and has certain practical application value.