The supplier selection is the key factor of supply chain cooperation. This paper firstly constructs the indicator system of the cooperator selection of the supply chain, and confirms the corresponding objectivel weight of each indicator. Then the relative advantage matrix and the relative disadvantage matrix between the projects are calculated by the improved ELECTRE-II method, and the modified synthesized weighted matrix between the projects and the net advantage value of each project are calculated in the next step. And then rank the suppliers according to the net advantage value of each project. Finally, the paper illustrates the rationality of the indicators system and the efficiency of the evaluation method through the usage in a case.