A small seepage could cause significant changes to the hydrodynamic gradient and further enhance the sediment incipient motion and scour. However, most previous studies either ignored the influence of seepage or only considered the upward seepage in the prediction of sediment incipient motion. In this paper, a modified Shields number considering the two-dimensional seepage was derived. The analytical solution and numerical model were used to analyse the influence of wave-induced seepage on sediment incipient motion. The results indicated that two-dimensional seepage promoted the sediment incipient motion near wave troughs and restrained it near wave crests. The influence of seepage on sediment incipient motion would be underestimated if the horizontal seepage force was ignored. Meanwhile, it was found that the lower water depth and saturation, higher wave height, shear modulus and permeability in z-direction would remarkably increase the seepage force and then enhance the mobility of seabed particles.