Aiming at the current problems of security threats and privacy leak risks in the operation process of related data of intelligent logistics system, and the operation of system lacking of supervision and traceability, this paper proposes to use blockchain technology to resolve these problems. A scheme on applying blockchain in intelligent logistics system is proposed, including operation principle, consensus authentication mechanism, and data storage and access mechanism. By introducing and analyzing the related big data of intelligent logistics system, improving the scientific, rationality, and intelligence of the decision. The basic characteristic of blockchain is traceability. By constructing algorithm models, proposing the realization principles of consensus authentication mechanism. For different events, different ''multi-authentication centers'', intelligent contracts, and blockchain systems are constructed, improving the efficiency and supervision of the operation of intelligent logistics system. By constructing the correlations between the fundamental data that corresponding to different blockchain, and the correlations between the fundamental data that corresponding to the same blockchain, making the related data easier to collect and analyze. By constructing the storage and access mechanism, ensuring the security and confidentiality of the operation data of intelligent logistics system. This paper has provided thought for the application research of intelligent logistics system based on blockchain, and has positive reference value and guiding significance to the development of blockchain application research.