According to a field measurement in 2012, the bathymetry in the area of Mailiao Harbor, located in the middle of Taiwan's west coast, has scouring hole with a size distribution of approximately 500x100 m. The maximum scour depth is 26 m (from -22 m eroded to -48 m). Although scour has become a major threat to breakwaters and navigational safety, it can be predicted cost-effectively, reliably, and rapidly by applying the computational fluid dynamics (CFD) numerical simulation. In this study, numerical simulation of tidal current and typhoon waves was performed to investigate the causes of the scouring hole in the Mailiao Harbor sea area. Current field data from an acoustic Doppler current profiler (ADCP) were used as the requirements of tidal boundaries. A fixed-bed bottom boundary was generated using sounding data from the year 1996, and the harbor computer-aided design (CAD) physical model was used as the requirement of the closing boundary. Moreover, the sensitivity of grid independence and numerical domain was tested to create a steady flow field. The study results indicated that a vorticity form at the lee side of the breakwater during tidal cycles conformed to tidal current data with numerical modeling. Furthermore, describe the distribution of fluid velocity, excess shear stress and tidal current by visualization, the application of scour potential model with the Stokes 5th order wave boundary is found to give more reasonable results.