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According to a field survey in 2012, the bathymetry near Mailiao Port, located in central Taiwan’s west coast, has a scouring hole that extends approximately 500 m × 100 m with a maximum scour depth of 26 m (eroded from its design depth −22 m to −48 m). To investigate the scour mechanism near the breakwater head and prevent the breakwater from collapsing, this study conducts comprehensive analysis by analyzing field observed data, performing hydraulic model tests, and conducting numerical modeling for the area near the Mailiao Port. The results show that the current plays an important role in the scour process. The physical model tests and numerical simulations both can reproduce the scour phenomenon of the study site. By analyzing field observed data we validated through physical and numerical models. This study concludes that the current caused by the ebb and flood tide, as well as the steep and shallow seabed topography, together comprise the seabed scour mechanism near the Mailiao Port breakwater head.