The informationization and intelligentization of modern agricultural logistic management has become the new conception of agricultural modernization and the inevitable trend of the development of worldwide agriculture. Based on the connotation and architecture of intelligent decision support system, it brings out the functional structure and architecture of intelligent decision support system of modern agriculture logistics, which mainly focus on the model base and knowledge base and assist with the research of data base, way base, and the intelligent decision support system of modern agriculture logistics of computer network technology. Moreover, this system has relatively sufficient function of predication and decision, in order to help decision makers to improve the level and quality of final decision.