Based on the Eulerian-Eulerian two-phase flow theory, the live-bed pier scour was carefully simulated with the consideration of suspended load. The riverbed variations were obtained using the non-equilibrium sediment transport model by calculating the mass exchange between the suspended load and traction load. By redeveloping a Computational Fluid Dynamics (CFD) software, i.e., ANSYS Fluent, the sediment transport rates and exchange flux between the suspended load and traction load were calculated using the shear stress of sediment and sediment concentration. By doing this, the riverbed boundary can be real-timely updated according to the calculated riverbed variations to conduct the live-bed scour simulation. The accuracy and rationality of the proposed simulation was fully verified by comparing with the classic theory and several experimental results from the viewpoints of the suspended load distribution, scour depth, and scour hole profile. The significant influence of the sediment concentration on the scour performance was finally proven by a parametric study. It can be concluded that using the live-bed scour models based on the two-phase flow theory should be very necessary for an accurate simulation.