Blockchain is naturally suited to food traceability systems because of its credibility and non-tamperability, and its application in the field of food traceability is increasing. However, when blockchains are applied in existing food traceability systems, many problems may arise. These problems include there being too many food traceability scenarios, large blockchain network loads, and long network delays. In response to these problems, we introduce the Interpretative Structural Modeling method layered idea to optimize the traditional Practical Byzantine Fault Tolerance (PBFT) consensus mechanism commonly used in blockchains, in order to improve the performance of existing traceability systems. We construct an explanatory structure model through the transaction relationship between the blockchain nodes, layer the blockchain consensus nodes, establish a layered system of blockchain consensus nodes, and then divide the layered blockchain consensus nodes into blocks. We then divide multiple sub-node clusters participating in the consensus and use multi-center sub-node clusters to implement the PBFT consensus. Finally, the consensus center node submits the consensus result to the block to achieve the overall consensus. The food traceability dataset was collected from the intelligent poultry house jointly established by the Beijing Municipal Bureau of Agriculture and Rural Affairs and the Beijing Animal Husbandry Terminus and the intelligent chicken house monitoring and management platform based on the alliance blockchain through the experimental verification of throughput and consensus time-consuming. The improved practical Byzantine fault-tolerant consensus algorithm realizes the multi-center sub-node cluster hierarchical and block consensus, and solves the network congestion problem in the traditional Practical Byzantine Fault Tolerance algorithm. It also reduces the blockchain network broadcast resource waste, reduces the blockchain consensus communication cost, and ensures the security of the blockchain consensus while improving the efficiency of the food traceability blockchain network communication and consensus.