The influences of two structures (upstream enterprisedominated and downstream enterprisedominated) on production, transportation and order policies are studied in two echelon supply chain under the incomplete information, since the enterprises usually obtain incomplete information from each other in reality. The cooperation motivations of enterprises are analyzed. The optimization models of cost before and after cooperation are built. By comparing the production, transportation and order policies before and after cooperation, we find out that the dominant enterprise’s policy is more probable to implement before cooperation and the cooperation motivations of the enterprises in downstream enterprisedominated structure is greater than the one in upstream enterprisedominated structure. The numerical experimentation illustrates the fact that cooperation can bring more benefits to both of enterprises, and it is an efficient operation model.