In order to study the effect of acceleration-skewed waves on the bottom boundary layer, a numerical model was developed to reproduce the velocity profiles, turbulent intensity, and bottom shear stress as measured in a physical model experiment. Based on this, the hydrodynamic characteristics of the boundary layer under the acceleration-skewed waves were examined. Numerical results show that greater flow acceleration in the positive accelerating stage within a wave crest half-cycle leads to quicker development of the boundary layer, a larger velocity gradient, and greater turbulent intensity, resulting in positive period-averaged bottom shear stress. These features become more pronounced when the degree of acceleration skewness increases. In the oscillating water tunnel, the time-averaged current velocities are positive and negative in the upper and lower regions of the boundary layer, respectively, and the negative near-bed current velocity increases with the degree of acceleration skewness. In the open sea, the time-averaged current velocity is positive over the whole boundary layer, velocity over-shooting is found in the lower region, the velocity is uniform in the upper region, and the positive near-bed current velocity decreases with the increase of the degree of acceleration skewness.