It is envisaged that boundary layers and bottom shear stress behaviors having the effect of acceleration in the wave asymmetry and skew-ness are different from those in sinusoidal waves. Therefore, the asymmetric and skew waves cause a net cross-shore transport of sediment over a complete wave cycle. In the present paper, a new calculation method of bottom shear stress based on incorporating velocity and acceleration terms is applied to the calculation of the sediment transport induced by cnoidal wave as representative of the non-linear wave. Moreover, the bottom shear stress calculation methods are examined through both a two-layer baseline (BSL) k-ω model and the experimental result on turbulent boundary layer for cnoidal waves. The acceleration effect on both the bottom shear stress and sediment transport under cnoidal waves are examined according to the wave non-linearity effect, respectively.