With the continuous development of economy and technology, the importance of logistics services has gained more and more attention in the whole industry chain. Collaborative operation between manufacturing companies and logistics companies can improve operational efficiency and save the cost for the enterprise by the way of simplify the transaction process in the supplying chain and reducing the transaction costs. In this paper, through the deep investigation and analysis of the collaborative operation between logistics and manufacture, combing the previous studies and opinions of the relevant professors, a series of evaluation indicator has been teased out, which is suitable for evaluating the collaboration performance. Meanwhile, a multistage fuzzy comprehensive evaluation system is constructed by using analytic hierarchy process and fuzzy comprehensive analysis method.