The cable-stayed bridge with steel-concrete hybrid girders is one of the most widely used bridge types in China. As the key sub-structure of this kind of bridge, the hybrid zone which consists of girders in the region jointing the steel girder and the concrete girder plays an important role securing the safety and good serviceability of the entire bridge, and consequently the study on the mechanical behavior of the hybrid zone is essential for both the analysis and design of the whole bridge. However, due to the strong dependence of the Saint-Venant Principle and significant influence of the Fuzzy Region which cannot be quantitatively determined, the traditional local-elaborate modeling method for the study is limited by its dim Saint-Venant Region-Fuzzy Region boundary, leading to unreliable analysis results and enormous trial and error works. To tackle this problem, the multi-scale modeling method is introduced in this paper, employing the flexible boundary conditions (flexible BCs) for the simulation of the complex boundary condition of the hybrid zone. The fourth dimension is time. In order to gain results closer to the realistic behavior of the bridge at the finished date, it is considered to model the construction process. A 4D multi-scale model of the hybrid zone is then established according to the prototype of an actual cable-stayed bridge project in Chongqing, China. Simultaneously, a local-elaborate model is built for comparison. Comparison study of the finite element models demonstrates that analysis results of the 4D multi-scale model are reliable without the influence of the Fuzzy Region. The model is more accurate, reliable and hence widely applicable. It is concluded that the 4D multi-scale modeling method may offer a new approach for the analysis and monitor of the hybrid zone for cable-stayed bridges with steel-concrete hybrid girders in the future.