In recent years, mass customization is an important issue in manufacturing industries. They may require a make-to-order (MTO) manufacturing system throughout the whole supply chain. Our previous researches proposed a basic three-layered supply chain model for dynamic configuration of supply chains including an MTO manufacturing system. The model consists of three model components named a client, a manufacturer, and a supplier. A negotiation process among the model components were proposed in order to enter into a lot of contracts. This paper presents a cooperative negation method between a manufacturer and a supplier. The objective is to provide a negotiation method for entering into a large amount of contracts with a client. A manufacturer adjusts the requirement of part order for a supplier by reallocating manufacturing operations backwards from the delivery time required by a client. We developed a prototype of simulation system for a three-layered supply chain. We carried out large number of computational experiments by changing experimental conditions and verified the effectiveness of the proposed negotiation method.