In view of drawbacks in supply chain of China’s traditional agricultural products, this paper proposed building supply chain system for modern agricultural products: taking informationization as basis, channel system as core, organization system as support, and service system and safety system as guarantee, to promote high efficient operation of the supply chain system. The channel system stresses alliance and integration of channel system, informationization of channel management, and terminalization of channel operation; the organization system stresses organization, large scale, group, and brand of participant entities; service system stresses construction of service means, service platform, and operation mechanism; safety system stresses building quality safety based agricultural product supply chain management mode. In order to ensure high efficient operation of supply chain for modern agricultural products, it is required to straighten out supply chain management system, actively cultivate core enterprises of supply chain, strengthen information construction of supply chain, select suitable supply chain mode, and improve benefit allocation mechanism.