To safely pass through the cross-river bridge, the large container ships built by shipyards along the Yangtze River are usually split into upper and lower parts to reduce their clearance height and towed across the bridge by tugboats from the Maritime Bureau. This method leads to expensive towing costs and longer hours for the reassembly of the superstructure. A new design scheme for the jack-up structure of a fully enclosed bridge is proposed for the self-propelled bridge crossing of the large container ships, greatly saving the costs and time. Additionally, the strength of the jack-up structure and the deformation of the navigation deck and window frame of the fully enclosed bridge are evaluated by using the Finite Element Method, verifying the safety and construction feasibility of the design scheme. This article can provide design references for ships with large clearance heights to achieve self-navigation under bridges.