The green development of the entire agricultural industry chain is not only an important way to enhance the competitiveness of agricultural products and promote the value-added of the agricultural industry but also an inevitable choice to improve the efficiency of resource utilization and ensure sustainable economic development from the perspective of the ecological environment. This paper defines the connotation and characteristics of the green development of the whole agricultural industry chain and deeply analyzes the development status, major challenges, and feasible paths of the whole agricultural industry chain in China. It has built a whole industry chain development model of “Internet + modern agriculture” and proposed a decentralized agricultural data management system based on the IoT to solve the problem of untraceable of traditional agricultural products and other data. The agricultural IoT system is designed with a unique blockchain double-chain structure, using the global hash chain and the mutual verification between the transaction chains in each partition. It proposes the PMCP protocol, which improves the performance of the system by producing blocks in parallel for several consensus groups in each consensus cycle. The experimental results show that the proposed model is queryable, traceable, and trustworthy for whole-life agricultural data, and the proposed model outperforms other schemes in terms of throughput and delay.