Waves and storm surges induced by strong typhoons pose a serious threat to the safety of sea-crossing bridges. In order to study the damage mechanism of the superstructure and the substructure of the small and medium-sized sea-crossing bridges under the combined action of storm surge and wave, and the affecting law of wave under different water levels during the storm surge on the substructure, the damage patterns of the small and medium-sized sea-crossing bridges induced by the combined action of typhoon storm surge and wave are investigated. Survey results show that the failure patterns of the superstructure of the small and medium-sized sea-crossing bridge under the action of storm surge and wave mainly include beam body dislocation, beam body shedding and beam body fracture. The main failure reasons are that the beam is forced to undergo unconstrained movement. The failure patterns of the substructure are mainly structural deviation, collapse and failure of the girder connection failure, and the main cause is large hydrodynamic effect and impact of superstructure. Subsequently, wave loads on bridge substructure are studied by CFD three-dimensional numerical simulation and an empirical formula of wave impact on pier under storm surge is obtained. Finally, based on the investigation and numerical simulation, some suggestions and measures are proposed for structural design and structural construction.