To study the seismic response characteristics of the seamless transfer subway station and improve the understanding of the seismic performances of such station structures, the shaking table test on a scale model of such station structure was carried out for the first time. The design of the shaking table test included the preparation of test models, the arrangement of measuring points, collection of testing data and the design of test working conditions. Then, the processes of the model test were simulated by three-dimensional finite element method. Through comparison between the numerical and measured results, acceleration responses of the model soil, strain and internal force responses of the structure model and soil pressure responses on the sidewall were analyzed. The results showed that the numerical results agreed well with the test data, which validated the rationality of the modeling method in this paper. For the structure model of the seamless exchange subway station, the structural exchange end had an obvious influence on the structural deformation, the structural internal force and its surrounding soils. When the distance between the station exchange ends exceeded 1.5 times station structural width, its effect basically disappeared. These conclusions can provide powerful support to the three-dimensional calculation method for the seismic analysis of complex subway stations and the anti-seismic design of such station structures.