In　this　paper,　a　novel　direct　time-domain　numerical　method,　called　the　FEM-SBFEM-SBPML,　is　proposed　to　study　the　wave　propagation　problems　in　soil-structure　interaction　(SSI)　system　with　complex　geometry　and　geological　condition.　In　the　bounded　domain,　the　structure　is　modeled　as　beam　element　based　on　the　finite　element　method　(FEM),　and　the　surrounding　truncated　soil　is　discretized　using　the　scaled　boundary　finite　element　method　(SBFEM)　combined　with　an　efficient　quadtree　mesh　generation　technique,　respectively.　In　addition,　a　solidmodified　beam　coupling　model　considering　the　eccentric　effect　of　the　tangential　traction　at　the　outer　surface　of　the　structures　is　implemented.　The　unbounded　domain　is　modeled　by　a　recently　proposed　scaled　boundary　perfectly　matched　layer　(SBPML)　method,　which　is　a　novel　high-accuracy　absorbing　layer　method　satisfying　the　radiation　condition.　As　a　result,　the　combined　FEM-SBFEM-SBPML　approach　is　capable　of　modeling　SSI　with　complex　geometries　and　soil　properties　automatically.　Some　benchmark　tests　are　conducted　to　illustrate　the　accuracy　and　efficiency　of　the　proposed　scheme,　and　a　vibration　analysis　of　a　soil-tunnel　system　is　further　presented　to　demonstrate　the　applicability　of　the　proposed　method　in　engineering.