Wall shear stress (WSS) plays a key role in maintaining glycocalyx function, gene expression, and structure. Experimental studies have discussed the relationship between the shedding of the endothelial glycocalyx (EG) and WSS. However, rare literature about how WSS affects the EG during cardiopulmonary bypass (CPB) was mentioned. This study aimed to investigate the correlation between the WSS of carotid arteries and shedding of the EG during CPB in humans. The WSS level was calculated in accordance with an equation. The plasma concentrations of heparan sulfate, syndecan-1, and nitric oxide were measured to reflect shedding of the EG at six time points. A negative correlation was observed between the peak wall shear stress (PWSS) and syndecan-1 (R= - 0.5, p< 0.01) and heparan sulfate (R= - 0.461, p< 0.01) during CPB. The WSS is closely associated with the components of glycocalyx shedding during CPB. The WSS produced by non-pulsatile flow during CPB may contribute to the degradation of EG.