Abstract:  The rapid development of inland economy and the special geographical location of Fujian and Taiwan have provided a chance for the exchange and cooperation on economy and trade between Fujian and Taiwan.And great achievements have been made in cooperation in the field of agriculture.This paper elaborated the agricultural supply chain type in the current cooperation between Fujian and Taiwan, and then built the integration model of agricultural supply chain between Fujian and Taiwan based on e-commerce platform, which would achieve the bidirectionality across nodes of the information flow in agricultural supply chain and the resource integration for the node enterprises in supply chain, thus to improve the supply chain efficiency of Fujian’s and Taiwan’s agricultural products and further deepen the agricultural cooperation between the two sides.