The studies and analysis of the pounding damage mode and the mechanism of the caisson during construction under the action of storm waves are carried out based on the pounding damage of the caisson during construction caused by the super typhoon Sarika. In this paper, a new method for the numerical analysis of a structural model is proposed, and is employed to analyze the pounding response of the caissons subjected to the storm wave loads. According to the new method, the simulation process is divided into two steps. In the first step, the wave propagation caused by the typhoon is simulated by the wave-generating tool of Flow-3D, and the time history of the wave force on the caissons is also recorded at the same time. In the second step, a refined finite element model is developed in analyzing the pounding response of the caissons under the action of storm waves, and the wave force time-story curves are applied to the caissons according to the measured data in the first step for further analysis of the structural pounding response using the explicit solver of LSDYNA. The whole simulation of the pounding response of the caissons during construction caused by typhoon Sarika is carried out. The simulated and analysis results show that the different wave direction results in the angle of the caisson collisions, which will lead to different damage modes for the caissons. And when the angle between the wave action direction and the front/back walls of the caisson is 60°, the measured pounding damage mode is in a good agreement with the field situation caused by the typhon Sarika.