In February 2008, high storm waves due to a developed atmospheric low pressure system propagating from the west off Hokkaido, Japan, to the south and southwest throughout the East Sea (ES) caused extensive damages along the central coast of Japan and along the east coast of Korea. This study consists of two parts. In the first part, we estimate extreme storm wave characteristics in the Toyama Bay where heavy coastal damages occurred, using a non-hydrostatic meteorological model and a spectral wave model by considering the extreme conditions for two factors for wind wave growth, such as wind intensity and duration. The estimated extreme significant wave height and corresponding wave period were 6.78 m and 18.28 sec, respectively, at the Fushiki Toyama. In the second part, we perform numerical experiments on wave-structure interaction in the Fushiki Port, Toyama Bay, where the long North-Breakwater was heavily damaged by the storm waves in February 2008. The experiments are conducted using a non-linear shallow-water equation model with adaptive mesh refinement (AMR) and wet-dry scheme. The estimated extreme storm waves of 6.78 m and 18.28 sec are used for incident wave profile. The results show that the Fushiki Port would be overtopped and flooded by extreme storm waves if the North-Breakwater does not function properly after being damaged. Also the storm waves would overtop seawalls and sidewalls of the Manyou Pier behind the North-Breakwater. The results also depict that refined meshes by AMR method with wet-dry scheme applied capture the coastline and coastal structure well while keeping the computational load efficiently.