The decentralization of blockchain technology greatly improves the trust relationship in the supply chain network. In view of the lack of trust, uncertainty, and asymmetry in the supply chain network, this paper integrates the blockchain technology to build a network dynamics model of trust representation, calculation, and propagation, and explores how the blockchain influences the supply chain network. The result indicates that the network scale increased by 115.89%, the network connectivity increased by 60.31%, and the average shortest path decreased by 4.95%, after the blockchain trust framework had been deployed in the agricultural supply chain. Meanwhile, the network topology performance such as degree distribution and average clustering coefficient were optimized to varying degrees. Taking agricultural supply chain as an example, the practical significance of topological change was explained. Overall, the blockchain trust mechanism improves the topology of the supply chain network by affecting the trust relationship between nodes.