A systematic design for a liner shipping network was addressed. Many practical features in real-world operations, including multiple types of containers, container transshipment operations, empty container repositioning, origin-to-destination transit time constraints, consistent services with the current network, and joint services with other liner shipping companies, were considered. Given a set of candidate ship routes, some of these routes had to be used, and the use of others was optional. A mixed-integer linear programming model was proposed for the selection of optional ship routes. The solution of this model provided the laden and empty container flow on the selected ship routes. On the basis of the results of this model, techniques were proposed for refining ship routes by changing existing routes, designing new routes, and removing some routes. A large-scale numerical test based on the global shipping network of a liner shipping company, consisting of 166 ports, was performed.