In nowadays’ world, frequently occurred agricultural food safety events have severely done harm to people’s health and directly initiated great trust crisis to governments and agricultural food enterprises, and the E-commerce as virtual economy can enlarge the trust crisis terrifically. As a result, to establish unified traceability information sharing platform of agricultural supply chain has become an urgent task for the related organizations. This paper begins with an exploratory research on design and realization of Agricultural Food Supply Chain Tracking System (AFSCTS) in E-commerce environment, which can provide a powerful technical support for timely tracing and finding the link where a agricultural food safety problem happens in the supply chain. This paper has 5 sections: the first to briefly introduce the concepts relevant to AFSCTS and the significance of this research; the second to analyze three key technologies (RFID technology, database integration technology and data security technology) utilized in AFSCTS; the third to elaborate on two key algorithms (traceability algorithm and data encryption algorithm) designed in AFSCTS; the fourth to design and implement AFSCTS based on three key technologies and two key algorithms, and the overall system frame and function structure are narrated detailedly in the paper; the last to apply the AFSCTS in Nanfeng county (the hometown of famous Nanfeng Orange in China) for tracing agricultural food, and the system implementation has achieved experimental success.