With the prosperous development of the railway and urban rail transit engineering in recent years in China, the integrated station-bridge structures have been the predominant structure types for the key stations. Owing to the lack of the special code for these structures, the seismic design for the integrated station-bridge structure must be catering to the existing Code for Seismic Design of Buildings and Code for Seismic Design of Railway Engineering simultaneously. But the design philosophy of the two codes above mentioned is essentially different. In this paper, taking the main structure of Beijing South railway station as an example, based on the universe software of Midas/Gen and Sap2000, the global structure model considering the multiple modes effect resulted from upper truss and the corresponding simplified model were constructed, respectively. The rationality of the simplified model was verified by comparing the results from the analysis of the natural vibration characteristics, spectral analysis and the dynamics analysis of time history. The plastic yielding mechanism and the seismic performance were researched in detail by the Pushover analysis (considering the multiple patterns of the lateral loading) and the incremental dynamic analysis (IDA) respectively. It was shown that the proposed simplified model could essentially reflect the behavior of the main structure under the designated earthquake. The Pushover analysis method based on the improved lateral loading pattern considering the multiple modes combination could be applied to evaluate the seismic performance of the integrated station-bridge structures.