As productions and deliveries of multiple products to multiple marketplaces have been increasingly popular, supply chain flexibility, which refers to an ability to deal with demand and capacity uncertainty, becomes an important issue in supply chain management. However, logistics costs have been largely neglected in the literature on supply chain flexibility structure. In this paper, we propose mathematical models to investigate the impact of the logistics costs on the optimal flexibility structure. We also conduct a simulation study and observe that logistics costs have a significant impact on the decision on supply chain flexibility structure. Such conclusion is also supported by the case study of a global car manufacturer, Honda Motors.