As the main food source of the world’s population, grain quality safety is of great significance to the healthy development of human beings. The grain food supply chain is characterized by its long life cycle, numerous and complex business data, difficulty defining private information, and difficult managing and sharing. In order to strengthen the ability of information application processing and coordination of the grain food supply chain under many risk factors, an information management model suitable for the grain food supply chain is studied based on the blockchain multi-chain technology. First, the information on key links in the grain food supply chain is analyzed to obtain privacy data classifications. Second, a multi-chain network model of the grain food supply chain is constructed, and based on this model, the hierarchical encryption and storage mode of private data as well as the relay cross-chain communication mode, are designed. In addition, a complete consensus process, including CPBFT, ZKP, and KZKP algorithms, is designed for the global information collaborative consensus under the multi-chain architecture. Finally, the model is verified through performance simulation, theory analysis, and prototype system verification in terms of its correctness, security, scalability, and consensus efficiency. The results show that this research model effectively reduces the storage redundancy and deals with problems of data differential sharing in traditional single-chain research, as well as provides a secure data protection mechanism, a credible data interaction mechanism, and an efficient multi-chain collaborative consensus mechanism. By attempting to apply blockchain multi-chain technology to the grain food supply chain, this study provides new research ideas for the trusted protection of data and information collaborative consensus in this field.