The cooperative game with coalition structure generally involves two levels of cooperation: in which the players first form a small coalition, and then participate in the cooperation of the big coalition as a whole. In the One Belt, One Road Initiative, small sized alliance groups often have a weak voice in participating in cooperation projects, so they are easily at the disadvantages of profit distribution and their cooperative enthusiasm are affected. Therefore, it is necessary to further study the cooperative game with coalition structure and its solution. Based on this, a new solution method (i.e., weighted Owen value) is proposed in this paper, which can consider the impact of small coalition size on the cooperation. Then, based on the cooperative game with coalition structure and weighted Owen value, we describe the multi-level and complex cooperation relationship in the One Belt, One Road Initiative. The possible range of profit distribution are gotten for the player in the cross-border cooperation projects. Thus, the proposed weighted Owen value can be used to get a possible profit distribution range for each participant in cross border cooperation projects, which may provide a theoretical decision basis for the cross border largescale projects.