Hybrid cable-stayed bridges consist of steel and concrete bridge segments, of which steel–concrete joints are of great importance and raise strong research interest. Due to the limitation of the traditional methods, i.e., the member finite element (FE) method and Mixed Dimensional Coupling (MDC) method, the present study proposes a substructure method to model long span bridges. The current application of the substructure method is to extract some specific parts of the whole structure to refine and analyze them. Different from the routine substructure approach, here the entire structure is modeled in detail and divided into many substructures. All the substructures are then condensed into super-elements except the concerned part. The application of the method is then illustrated through numerical studies of the vehicle–bridge coupling vibration of the Jingyue Yangtze River Bridge with a main span of 816 m. The entire bridge is first divided into many substructures with a reasonable length. Among them, the concerned substructure with 23.8 m in length including the steel–concrete joint is modeled in detail but not formed into super-element, while all the other components are modeled in detail and formed into super-elements using the component mode synthesis (CMS) method. All the components including both the super-elements and non-super-elements are then assembled into a complete and fine full bridge model. Finally, the model is used for the vehicle-induced dynamic analysis under deterministic traffic flows. The results show that the joint works well, and the transition between the steel girders and concrete beams is very smooth.