Based on Finite Volume Coastal Ocean Model (FVCOM), this study constructed a numerical model covering the Bohai Sea, Yellow Sea, and East China Sea. National Centers for Environmental Prediction’s Climate Forecast System Reanalysis (NCEP-CFSR) data were used to drive the model to simulate a large storm surge generated by Typhoon Chan-hom. The model was validated by multiple in situ observations of water levels taken at tidal gauge stations. The effects of the nonlinear terms and topography on the modeling of storm surges were then studied. First, the tide–surge interaction during the storm surge process was analyzed. The results show that the tide–surge interaction can suppress the storm surge at the climax of the astronomical tide and benefit the growth of the storm surge at the ebb of the astronomical tide. The tidal constituents M2, S2 and K1 were added to analyze the influences of the amplitudes and periods of tides on the nonlinear reaction. The results indicate that the nonlinear effect will be enhanced by an increased tidal height; additionally, the nonlinear interaction of semidiurnal tides is more significant than that of diurnal tides. The semidiurnal fluctuation that appears near the peak-value time is also attributed to the tide–surge interaction. Moreover, the tide–surge interaction can be influenced by the water depth and position of the area of interest. According to the numerical results, topography has a certain impact on the storm surge: The peak value of the storm surge will decrease with increasing slope. The existence of the Ryukyu Islands reduces the area influenced by the storm surge on the southeast coast of China but expands the high-value storm surge area.