This　study　firstly　investigates　the　seismic　intensity　measures　(IMs)　from　the　existing　scalar　ones　that　are　suitable　for　the　prediction　of　seismic　response　of　shallowly　buried　rectangular　underground　structures.　The　peak　acceleration　and　peak　velocity　at　the　ground　surface　are　identified　as　the　optimal　IMs　based　on　their　efficiency,　practicality,　and　proficiency.　A　series　of　seismic　fragility　curves　are　then　developed　for　a　two-story　and　three-span　underground　subway　station　embedded　in　three　different　typical　engineering　sites　using　nonlinear　incremental　dynamic　analyses.　In　this　study,　the　input　ground　motions　at　the　level　of　engineering　bedrock　for　the　underground　structure-soil　interaction　system　are　obtained　through　one-dimensional　equivalent　linear　site　response　analysis　according　to　the　one-dimensional　wave　propagation　theory.　Comparison　of　the　numerical　results　in　this　paper　with　the　previous　empirical　and　numerical　fragility　curves　shows　that　the　fragility　analysis　method　in　this　paper　is　feasible,　which　can　quantitatively　give　the　failure　probability　of　structures　at　different　performance　levels,　and　can　provide　reference　for　seismic　design　of　underground　structures.　The　numerical　results　indicate　that　both　the　characteristics　of　ground　motions　and　the　site　profile　have　significant　influence　on　the　seismic　fragility　curves　of　underground　structures.　Underground　subway　stations　are　generally　more　vulnerable　to　seismic　damage　when　embedded　in　engineering　sites　with　lower　average　shear　velocity.　Moreover,　seismic　damage　margin　ratios　are　proposed　for　the　underground　structure　in　different　site　classes　to　show　the　confidence　levels　of　its　seismic　performance　when　subjected　to　different　levels　of　earthquake　events,　and　can　be　used　as　a　preliminary　index　for　the　earthquake　risk　assessment　of　subway　station.