The causes of foundation scour of sea-crossing bridges are complicated. To prevent water damage, it is critical to investigate the local scour situation these bridges face at different construction stages. Taking the main pile foundation of Hangzhou Bay Railway Bridge (under construction) as the case study, we investigated the scour features and hydraulic characteristics of the bridge during different foundation construction stages by physical model test, numerical simulation and in-situ measurements. The results show that the model test and numerical simulation results are consistent with the measured data. During the pile foundation construction stage, the tidal waves and torrents have scoured the sandy layer off, left the bridge site surface with a muddy clay layer, which is more difficult to be soured off. 70% of the scour depth occurs in the first 30% of the scour duration. The cofferdam can reduce the relative variation range of shear stress on the bed surface and the surrounding flow velocity, resulting in the formation of a silting area on both the stoss and lee side. After the cofferdam is lowered, the scour depth will continue to grow another 4 m, which can further increase the scour depth and scope by about 30%, exceeding the designed scour depth of pile foundation. Therefore, countermeasures should be considered for scour prevention and foundation protection. The research results can provide a reference for the design, construction and operation management of similar sea-crossing bridges.