The opening of the Metaverse era has gradually changed the ways of production and distribution of human society. The highly virtualized immersive Internet world has become a new stage of the development of the next generation of the Internet. The “food, clothing, housing and transportation” in the Metaverse are also an essential elements of life and important fields for virtual citizens. However, as a new form of integration of a variety of cutting-edge information technologies, the Metaverse is currently less studied and applied in agricultural related fields. This paper analyzes the value of the social attribute and digital asset attribute of virtual food in the Metaverse, discusses the significance and application scenarios of food traceability in the Metaverse, and builds a Metaverse traceability system based on the perception layer, data layer, basic layer, tool layer, and application layer. This system targets operation and maintenance management client, merchant enterprise client and consumer user client, and designs the main functions such as authority management, blockchain management, smart contract management, platform operation and maintenance, food processing management, data collection management, product traceability, claim and planting, as well as the supporting front-end and back-end development technology routes. It describes the working principle of smart contract as the core technology in the process of Metaverse food traceability. A set of design ideas and deployment process of smart contract are proposed. This system is an innovative exploration of cross-border integration between agricultural industry and other new technology scenarios such as blockchain and Metaverse. It is forward-looking and applicable, and provides guidance and reference for future research on the application of Metaverse in agriculture.