<p>Based on the OpenSEES program, a comprehensive numerical framework was established based on Biot′s u-p formulation to simulate the dynamic interaction between subway station structures and saturated soil media. The proposed model effectively characterizes the seismic behavior of two-phase porous systems. Through systematic parametric investigations, this study provides critical insights into how the spatial configuration of saturated soft interlayers, particularly their depth and thickness, influences the seismic performance and structural failure patterns of underground stations. The numerical results show that: (1) the amplitude of acceleration response spectrum in soft interlayer or upper soil layers decrease and the spectrum pattern shows significant agglomeration phenomenon within the long-period range; (2) the predominant area of the peak values for excess pore water pressure enjoy tremendously significant when the depth of the soft interlayer is equal to the height of station′s structure, and it may lead to the further expansion of the predominant area to the ground surface with the increasing thickness of the soft interlayer; (3) the dynamic internal forces in the most disadvantageous sections of structure reach the peak value when the depth of the soft interlayer equals the height of station′s structure, and the peak values of the dynamic internal forces in the most disadvantageous sections vary non-monotonically with the increasing thickness of the soft interlayer.</p>