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The reason why medical logistics cost remains high is a system problem, this paper analyzes the system through the ISM model. The result presents that medical logistics cost factors have four levels of relationship, primary factor is the national policies, secondary factors are the talent construction and pharmaceutical enterprise scale, Intermediate factors are medical information management system and inventory cost, the key factors are transportation cost and distribution center location. Finally, according to the four levels of relationship, this paper put forward specific suggestions to reduce logistics cost.