During earthquake events, a mainshock may trigger a number of following aftershock earthquakes in a short time. Usually, structures will be damaged to a certain extent by the mainshock, and aftershocks can further exacerbate the damage to structures, making post-disaster rescue and rehabilitation extremely challenging. Yet, most of research on seismic performance of underground structures only considered the single mainshock, ignoring the effect of aftershocks. In this study, a nonlinear numerical model of the shallow buried shallow subway station in clayey sand soil under mainshock-aftershock sequences was constructed to replicate the damage evolution process of underground structures. A limited numerical sensitivity analysis was performed considering the influences of the magnitude of mainshock and aftershock intensity. The results indicate that the damage of subway station is closely related to the magnitude of mainshock intensity. The aftershocks might cause more serious incremental damage to underground structures and secondary displacement of the site, potentially lead to collapse of the subway station, when the mainshock magnitude is greater. With the superposition of the mainshock and aftershock, the relative horizontal displacement of the subway station could reach the inter-story drift limit value. Therefore, the aftershock should be taken into account for seismic safety design of shallow underground structures.