Shipping enterprises are the organizers of container transportation. Their choice of routes and ports directly affects the construction of container network. In this paper, using the schedule data, 18 of the top 20 shipping enterprises are selected as the research objects to analyze the similarities and differences of their route network patterns, and to explore the influencing factors of their route configuration. We can find that, the route network of each enterprise has the characteristics of small world and scale-free, which means that it is controlled by a small number of highly connected hub ports. East Asia is the primary agglomeration area for each company’s schedule. Singapore, Shenzhen, Busan, Hong Kong and Shanghai occupy an important position in the route network of each company. And the enterprise route network shows a certain hub-and-spoke feature, which is a hybrid network where the hub-and-spoke connection and the point-to-point connection coexist. The differences of their networks are as follows: the market coverage and depth of each enterprise varies greatly, shipping giants such as Maersk and Mediterranean take both breadth and depth into account, CMA CGM and ZIM focus on market breadth, while Korea Marine Transport Company and Hamburg Sud tend to dig deep into the regional market; there are large differences in the spatial distribution of each company’s schedule, according to which, the shipping enterprises can be divided into four types, and as one of the types, Korea Marine Transport Company, Hamburg Sud, United Arab Shipping Company and Wan Hai Lines focus on specific regional market segments; the hub ports chosen by shipping enterprises are quite different, and some enterprises such as Korea Marine Transport Company and United Arab Shipping Company have their own hub ports that are not global hubs. The route configuration of shipping enterprises is affected by a variety of factors, such as source of goods of port hinterland, natural conditions and operation efficiency of ports, maritime protection policy, and enterprise scale and port investment. This study enriches the theory of transport geography, and reveals the route organization mode of shipping enterprises, which can provide guidance for the decision-making by port managers.