The problem of the wave-seabed interactions around a pipeline has become an important issue in the field of coastal geotechnical engineering, due to the exploitation of oil and gas industry. To date, most existing studies adopted one-way coupling algorithm to integrate wave and seabed sub-model, which violated the physical phenomena. In the study, a new two-way coupling algorithm for the wave–seabed interactions around a pipeline is proposed. The numerical results indicate that the water surface elevation, pore-pressures, soil displacements and effective normal stresses obtained by two-way coupling model are smaller than that of the conventional one-way coupling model generally. However, the Shields number by two-way coupling model is extremely larger than that of one-way coupling model, which implies that two-way coupling is required for the prediction of the scour. Meanwhile, the existence of pipeline would increase the influences of two coupling models on wave and seabed characteristics.