This study explores the discrepancies of storm surge predictions driven by the parametric wind model and the numerical weather prediction model. Serving as a leading-order storm wind predictive tool, the parametric Holland wind model provides the frictional-free, steady-state, and geostrophic-balancing solutions. On the other hand, WRF-ARW (Weather Research and Forecasting-Advanced Research WRF) provides the results solving the 3D time-integrated, compressible, and non-hydrostatic Euler equations, but time-consuming. To shed light on their discrepancies for storm surge predictions, the storm surges of 2013 Typhoon Haiyan in the Leyte Gulf and the San Pedro Bay are selected. The Holland wind model predicts strong southeastern winds in the San Pedro Bay after Haiyan makes landfall at the Leyte Island than WRF-ARW 3 km and WRF-ARW 1 km. The storm surge simulation driven by the Holland wind model finds that the water piles up in the San Pedro Bay and its maximum computed storm surges are almost twice than those driven by WRF-ARW. This study also finds that the storm surge prediction in the San Pedro Bay is sensitive to winds, which can be affected by the landfall location, the storm intensity, and the storm forward speed. The numerical experiment points out that the maximum storm surges can be amplified by more 5–6% inside the San Pedro Bay if Haiyan’s forward speed is increased by 10%.