In this paper, we study the interdependent order allocation problem in the many-to-many supply chain, which the demands from demanders are interdependent orders. We also consider the ability constraints of suppliers and different order issues such as the execution time, the quantity and the cost. In order to resolve the conflicts caused by the interdependent orders and simultaneous orders, the automated negotiation approach is adopted. Firstly, the interdependent order allocation problem is defined. Then, the two-stage negotiation protocol and various negotiation strategies are developed. The negotiation protocol integrates the bidding negotiation and the argumentation-based negotiation to support the interactions between the manufacturers and the suppliers, and also prescribes the rules of negotiation that regulates the interaction acts while the negotiation strategy guides the negotiation partners’behavior. The simulation experiment verifies that the order allocation problem can be resolved through the automated negotiation. It also numerically analyzes and compares the order allocation performances under different supply chain contexts. The experiment results show that the order allocation can be resolved through the negotiation under different supply chain contexts.