The seismic response characteristics of underground structures are very different from those of aboveground structures. Great efforts have been made in investigating the influence factors on the seismic responses of rectangular underground structures, while the theoretical analyses and comprehensive understandings remain insufficient in the current research. In order to shed light on the seismic response characteristics of the shallow buried rectangular underground structure, an extended parametric study, based on a real underground structure, the Daikai subway station in Japan was conducted in the present paper. In particular, a two-dimensional soil-structure system was adopted for the dynamic time-history analysis. The equivalent linear model was used to consider the nonlinear behaviors of the soil elements, and the elastic model was used to simulate the structure elements. A variety of critical factors that may significantly affect the seismic responses, such as: (i) earthquake load condition, (ii) structure inertia effect, (iii) soil inertia effect, (iv) soil-structure relative stiffness, and (v) soil-structure interface properties were comprehensively investigated in this study. The variations of the horizontal relative deformation between the top and bottom slabs of the structure and the internal forces of four representative sections that were most concerned in seismic design were calculated and compared in different cases, and the soil pressures and shear forces around the structure were also systematically discussed. The numerical results indicated that the seismic responses were obviously affected by the soil inertia effect and soil-structure relative stiffness, and more attentions should be paid to these critical factors during the seismic design of the underground structure. The presented results can lead to better understandings on the seismic responses of the shallow buried rectangular underground structure and can provide some improvements to the existing simplified methods and guide the seismic design of the underground structure.