The shipping market is unpredictable and volatile due to some uncontrollable factors such as epidemic, conflicts and natural disasters. There is always an imperfect match between the supply capacity of liner companies and the actual demand of the market, which leads to a waste of slot resources and/or unsatisfied customer demand. Furthermore, the trade off between empty container transportation and laden container transportation is the crucial problem of strategic importance for liner companies. To deal with the above problem, this paper aims to develop a new solution to the collaborative optimization problem of container slot allocation and empty container repositioning by exploring the resource allocation, storage, and repositioning methods collaboratively. An online booking platform is introduced in this paper, and no-shows and customer preferences are considered in the analysis. An innovative integer programming model is established based on an online booking mode and a delivery-postponed strategy. A new branch-and-cut algorithm is then proposed to solve the problem. Finally, numerical experiments are conducted to verify the effectiveness of the proposed model and algorithm. The experimental results show that collaborative optimization can remarkably enhance the revenue of liner companies along with increasing the utilization of slot resources.