This paper focuses on the single-issue negotiation between Manufacture Agent (MA) and Material Supplier Agent (MSA) of the supply chain. MSA resorts to find partners to cooperate when it cannot finish the order independently. A two stage negotiation protocol is proposed. The cooperative game is combined with MA-Stackelberg game to resolve the negotiation problem. It is used to establish the coalitions. Then, the final determined coalition negotiates with MA to reach an agreement using the Stackelberg game. Protocols without concession and with concession are respectively discussed. Simulations and comparisons are provided to verify the effectiveness and superiority of the proposed protocol.