The　three-dimensional　(3D)　equivalent　viscoelastic　boundary　element　is　introduced　based　on　the　theory　of　viscoelastic　artificial　boundary.　The　wave　input　method　of　wave　scattering　problems　in　free　field　is　stated　and　used　in　3D　layered　half　space.　The　seismic　waves　can　be　transformed　into　equivalent　forces　adding　on　the　artificial　boundary　nodes.　The　equivalent　forces　are　calculated　by　finite　element　model　with　lumped　mass　and　finite　difference　method.　A　3D　finite　element　model　of　soil-structure　interaction　system　is　built　in　the　platform　of　ABAQUS　software.　Seismic　responses　of　subway　station　structure　are　analyzed　including　factors　that　influence　it.　The　open　system　is　turned　to　a　closed-system　by　adding　local　artificial　boundary.　The　modal　characteristics　of　the　soil　and　station　are　obtained　by　modal　analysis.　The　seismic　responses　of　the　subway　station　structure　in　horizontal　and　vertical　directions　are　analyzed　under　SV　and　P　waves.　The　corresponding　regulations　and　distribution　of　internal　force　are　studied　to　examine　the　most　vulnerable　positions.　The　results　show　that　the　SV　waves　inputted　in　transverse　direction　is　the　worst　case　to　the　subway　station.　The　forces　of　the　members　suddenly　changes　in　position　at　where　the　stiffness　of　the　structure　is　changed　greatly.　The　P　waves　have　greatly　effect　on　the　axial　force　of　the　structure.