The　seismic　responses　of　offshore　structures　and　dams　can　be　affected　by　the　water-structure　interaction.　The　structures　are　commonly　modelled　by　finite　element　method　(FEM).　If　the　infinite　water　layer　is　also　modelled　by　FEM,　then　the　computational　costs　are　high.　In　this　paper,　an　accurate　and　efficient　substructure　method　is　presented　in　a　frequency　domain　for　a　2D　water-structure　interaction　analysis,　in　which　the　modified　scaled　boundary　finite　element　method　(SBFEM)　is　applied　at　a　general　shaped　water-structure　interface　to　replace　the　compressible　water　layer.　Several　numerical　examples,　including　offshore　structures　and　a　typical-geometry　gravity　dam,　are　provided　to　demonstrate　the　computational　efficiency　and　accuracy　of　the　proposed　substructure　method.　The　effects　of　hydrodynamic　pressure,　water　compressibility　and　structure　geometry　on　the　seismic　responses　of　offshore　structures　are　analysed　based　on　the　proposed　method.