Based on the governance structure of relationships, the agricultural supply chain can be characterized into five types: a more stable relationship with partners, the partner of choice of non-contractual stable relationship, formal contractual relations, strategic alliances based on relationship and strategic alliances based on property rights. The quality safeguard mechanism of agricultural product is not same in different supply chain organization. Close relationship can improve the safety and quality of China’s agricultural product. In cooperation of agricultural supply chain, formal mechanism and informal mechanism are all important to guarantee the product’s quality and safety. Formal mechanism includes legally binding contract, information sharing mechanism and joint decision-making mechanism. Informal mechanism includes trust, communication and so on. Currently, the number of participants of agricultural supply chain organization is increasing, the relationship shows a close characteristic, but China's agricultural supply chain organization is still at a low level, we should promote it to a higher level through increasing the support of government, enhancing core business capabilities and optimizing cooperation mechanisms.