Quality-related data collecting by the Internet of things sensing device was added to the blockchain, which could solve the problem of data being easily tampered and increase the data credibility in the storage link. However, data stored directly in the blockchain can result in low system throughput and long response time. The dual storage design of “database + blockchain” can greatly improve the response speed, but its response speed still cannot meet the demand. Aiming to improve the dual-storage design of “database + blockchain” by using the method of data Hash value secondary chain and verification based on the characteristics of fruit and vegetable quality traceability. The time complexity of the improved method was reduced from linear order to constant order in terms of data query. The results showed that the efficiency of the improved method was greatly enhanced. The average query time was 0.066s. And the query time could remain constant as the increase of data items, which solved the problem of low query efficiency for the application of blockchain technology in the fruit and vegetable quality traceability system. According to Hyperledger Fabric platform, the improved method was used to realize the development of fruit and vegetable quality traceability system, which achieved good demonstration effect when it was applied to fruit and vegetable enterprises.