The bottom shear stress estimation under sawtooth wave is the crucial step, which is required as an input to most of sediment transport model under rapid acceleration and the contribution of pre-suspended sediment to the onshore sediment transport in swash zone. Suntoyo et al. (2002) had shown that the bottom shear stress variation under sawtooth wave was dependent on high acceleration and deceleration. However, investigation of a more reliable calculation method to estimate the time-variation bottom shear stress under sawtooth wave over rough bed has not deeply done yet. In the present study, turbulent bottom boundary layer flow under sawtooth wave is investigated with the experiments in oscillating wind tunnel over rough bed by laser Doppler velocimeter (LDV) to measure velocity distribution. Bottom shear stress will be estimated by fitting the logarithmic velocity profile to the measured velocity. Furthermore, the experimental results will be examined with the bottom shear stress calculation method based on both the consideration of the friction coefficient for sinusoidal wave motion and that of the acceleration effect for sawtooth wave.