Abstract: Sediment transport under nonlinear waves is a hot research topic in coastal engineering. Wave profile and free surface wave effects are recognized as important factors in sediment transport. Due to the difficulty of constructing large-scale wave flume and corresponding wave generation, most experiments and numerical studies on sediment transport are carried out upon an oscillating water tunnel, and few results are obtained from wave flume. In comparison with a traditional oscillating water tunnel, the wave flume performed both wave profile and free surface wave effects on sediment transport in nearly real scale situation. A numerical wave-sediment flume is constructed for strongly nonlinear propagation of wave over sediment bed with low computational work. The nonlinear wave is generated by boundary wave maker and absorbed by a damping function, and classical VOF method is used to handle the free surface. The near-bed sediment condition for asymmetric wave is extended to the two-dimensional flume, which introduces phase lag, mass conservation, acceleration effect and asymmetric boundary layer development. Therefore, complex calculations for near-bed high sediment concentration in a two-phase model are avoided, i.e., the computation of particle collision, friction, and detection of mobile bed surface. In addition, the particle wake vortex effect and the relative velocity modification of non-static high sediment concentration are considered in sediment transport. The numerical wave flume successfully simulates the sediment transport under strong nonlinear second-order conical waves, and its reliability is verified by the large-scale wave flume experiment and the two-phase model including free surface waves. Comparison of the results of the numerical wave flume with the oscillating water tunnel shows that the presence of additional onshore streaming under the influence of free surface waves significantly enhances the onshore sediment transport.