Provided is a supply chain optimization system and a method for optimizing a supply chain that can prevent a production delay due to the lack of materials and a shipment delay due to the lack of stock products even if a sales plan fluctuates on an increase in sales of the supply chain as a whole and that can optimize the stocks of the products and materials and a physical distribution route of product supplies. The supply chain optimization system and the method for optimizing the supply chain calculate through a simulation in which a supply chain model is used so that a total sum of stock costs for products and materials and logistics costs therefor are minimized with respect to the number of stock products and materials which do not cause product defects at a fluctuation time of a sales plan on a condition in which the stock products increased in accordance with the fluctuation of the sales plan are set to factory stocks. Further, number of the stocks, costs for the stocks and logistics costs are set to a KPI of the supply chain to be managed. In addition, a physical distribution route from a factory increased in the stock products is optimized through the simulation.