An　artificial　boundary　element　and　equivalent　loading　method　are　introduced　for　considering　the　non-uniform　seismic　ground　motion.　Free　field　finite　element　is　built　to　verify　the　correctness　of　the　input.　Taking　a　subway　station　under　construction　in　the　background,　the　3D　finite　element　model　of　the　subway　station　was　established,　the　different　seismic　wave　spectrum　under　the　working　condition　of　uniform　and　non-uniform　wave　incident　seismic　ground　motion　response　of　a　subway　station　was　calculated,　and　the　subway　station　under　the　effect　of　non-uniform　seismic　response　characteristics　was　analyzed.　The　responses　of　subway　station　under　spatially　non-uniform　ground　motion　are　summarized　and　internal　forces　of　weak　positions　studied.　It　concludes　that　the　non-uniform　factor　needs　to　be　considered　for　the　long　span　subway　stations.　An　advice　of　anti-seismic　is　come　up　with.　©　2015,　Science　Press.　All　right　reserved.