Abstract: To reduce the distribution cost of empty containers, this paper presented an integer programming allocation model of empty containers by sea transportation for liner operators’ cooperation. The model is based on the allocating resources shared in liner operators, and at the same time considers the factors, such as rent cost, transporting cost, shipping direction, shipping capacity and reachability. The optimization objective is, when all liner operators who participate in the cooperating allocation can guarantee the shipping of the full containers and use each other’s allocating resources, to minimize the comprehensive obtaining cost for satisfying all empty containers demands which include allocating and renting empty containers. The model is followed by a numerical example, with an optimized scheme of empty container allocation by sea transportation for liner operators’ cooperation, to show that the model is practical and efficient.