The present work serves to improve the stable cooperation relationship among subjects of supply chain such as enterprises, farmers, intermediary organizations, and retailers and enhance the governance and optimization of agricultural product supply chain, thus strengthening the competitiveness of China’s agricultural industry. The supply chain governance of agricultural products is taken as the research object. Initially, the stabilities of two supply chain organization modes, “company and farmer” and “company, intermediary organization and farmer,” are analyzed by static game analysis. Then, based on the above analysis and the characteristics of blockchain institutional technology, a detailed analyzation is made on the mechanism of supply chain of agricultural products governance based on blockchain technology. Finally, the functional framework of agricultural supply chain governance is designed based on the basic framework of blockchain technology, and analyzation is made on the trust mechanism and contract mechanism of agricultural supply chain governance based on blockchain technology. The research results show that problems such as information and cognitive constraints in agricultural supply chain governance cannot be completely solved only through the evolution of blockchain organizational structure and the supply of governance mechanism, and speculative behavior will still appear. Optimizing the governance of supply chain of agricultural products based on blockchain technology can realize the transformation of its governance scenario. Meanwhile, the blockchain technologies such as deintermediation, demistrust, and intelligent contract play an important role in the process of agricultural supply chain governance, which can make it change in many aspects such as organization mode, application operation, and governance mechanism. The rapid development of new generation information technologies such as blockchain, the Internet of Things, and computer technology makes it possible to comprehensively digitize economic activities such as production and transaction in the supply chain of agricultural products. The present work combines the technical logic of blockchain digital governance with the institutional logic of agricultural product supply chain governance and tries to solve the instability problems caused by imperfect organization, lack of trust, and incomplete contract in agricultural product supply chain governance with the characteristics of blockchain such as deintermediation, demistrust, and intelligent contract.