In the existing market, companies confront a fierce competition, so the need for new and efficient process for supply chain has become necessarily important. To this end, supply chain management among multi agent system is proposed for addressing the selection and evaluation process related to the inbound logistics. However, most of recent systems deal solely with the negotiation including the selection of one or multiple suppliers, without supporting the transportation provider selection simultaneously and consider it as decision criterion that affect the final choice of cooperative suppliers. As part of win-win negotiation, active supplier involvement can enhance efficiency and effectiveness of supply chain. Then again, transport cost constitutes the most important factor in the third of the total operational costs of a supply chain. To face this challenge, a new form of supplier selection including transportation provider selection is proposed. For this purpose, we present a multi-issue decision protocol based on ontology to support the negotiation between upstream nodes of supply chain in the proposed multi agent system. Furthermore, the automated multi-criteria analysis model based on combined analytical hierarchy process (AHP) and TOPSIS is judged helpful for decision-makers to make quick decision with less human interactions.