In this study, we observe morphological changes of the coast with submerged breakwaters during the typhoon period and analyze the flow characteristics using the SWASH model. The study area is Bongpo Beach, located in Goseong, Gangwon-do, where three submerged breakwaters were completed through a coastal improvement project due to serious erosion problems, and the coast is affected by waves from the open sea. As a result of analyzing the changes before and after the typhoon period to identify places particularly vulnerable to erosion after the structures were installed, it is expected that the 2-cell circulation pattern is dominant for coastal flows. To predict the flow mechanism that caused these results, the wave data of the period is input as the offshore boundary condition, and the simulation is performed by dividing the layers in the vertical direction. As a result of simulating a total of 10 cases, the factor determining the overall pattern is the wave direction, and it is reproduced similarly to the observation results at the layer closest to the surface and bottom. Wave conditions are broadly classified into two types: shore normal wave incidence (ENE series) and oblique wave incidence (ESE series). We think that the difference in flow speed caused by the ESE series wave had a big effect on the area near Cheonjin Port where erosion was strong (more than 1.5 m) and that the ENE series wave dominated the rest of the area. These results are underestimated when the depth-averaged mode is applied. This suggests that multi-layered simulation is necessary to simulate complex coastal flows. Also, we think it will be used as a basis for figuring out how to deal with areas along the coast with submerged structures where erosion happens a lot because of the waves.