The effects of modified sea-surface roughness length over shallow waters are examined in a regional climate simulation over East Asia centered on the Korean Peninsula, using the Advanced Research Weather Research and Forecasting model (WRF-ARW). The control experiment calculates the sea-surface roughness length as a function of friction velocity based on the Charnock relationship. The experiment considering water depth in the sea-surface roughness length over shallow waters is compared with the control experiment. In the experiment considering water depth, the excessive near-surface wind speed over shallow waters is reduced compared to that of the control experiment. Wind speed is reduced also in the lower troposphere. The effects of modified surface roughness over shallow waters are not localized to the lower troposphere but extended into the upper troposphere. Through the vertical interaction between the lower and upper levels, upper tropospheric wind—which is underestimated in the control experiment—is enhanced in the experiment with modified sea-surface roughness length, not only over the shallow waters, but also over the entire domain. As a result, the vertical shear of zonal wind increases, leading to the enhancement of the negative meridional temperature gradient in the mid troposphere.