Wave-induced liquefaction depth is a key factor in providing the safe design of submarine pipelines. However, existing numerical studies simplify the seabed as a flat foundation and ignore the effect of scour depth on wave-induced seabed response and liquefaction depth. The effects of scour depth on wave-induced seabed response and liquefaction depth around a submarine pipeline are investigated, and a three-dimensional hybrid model combining Reynolds-averaged Navier-Stokes (RANS) equations with Biot's poroelastic theory for wave propagation and anisotropic seabed is proposed in this study. Numerical results indicate that local scour leads to the redistribution of the initial effective stress within the seabed around the pipeline. With increasing scour depths, the maximum liquefaction depth beneath the pipeline simultaneously decreases. When the scour depth reaches a certain depth, the seabed seems to no longer liquefy. Parametric studies indicate that the liquefaction depth increases by either decreasing the saturation degree or increasing the wave height. Under anisotropic seabed conditions, a nonlinear relationship exists between the maximum liquefaction depth of the seabed and the seabed permeability.