Abstract Underground structures such as subway stations, which are operated at a high capacity and frequency, are prone to damage by large earthquakes. To study the seismic performance of underground structures, this paper presents a three-dimensional nonlinear finite element simulation of the seismic behavior of subway stations, considering the influence of vertical ground motions and structural overburden depth. The results show that the consideration of vertical seismic motions increases the structural seismic responses; the influence extent depends greatly on the characteristics of the vertical seismic excitation. The station′s overburden depth influences the structural response significantly and alters the structural resonant frequency; the influence of the structural burial depth is a complex problem. Besides, it is deduced that the influence of structural burial depth tends to vanish with an increase in the induced frequency, particularly for deeper stations; more attention should be paid to deeper structures built on soft sites or deeper structures that suffer from long-period seismic shaking; the stiffer tunnel experiences less deformation, and the lateral earth pressure applied on the stiffer tunnel is higher. A few results in this paper are consistent with a damage survey of the Daikai subway station damaged in the 1995 Kobe Earthquake.