Considerable efforts have been devoted to the topic of wave–seabed interactions in the last two decades because of growing offshore activities. The existing studies have based on one-way coupling approach. In this study, a new two-way coupling algorithm is proposed to overcome the contradiction at the fluid–sediment interface between physical process and the existing theoretical models. The numerical results indicates that the seabed responses obtained by the two-way coupling model are slightly lower than that of the one-way coupling model. However, the two-way coupling model significantly affects the Shields number that would further affect the scour process. Parametric analysis indicates that larger wave height, current velocity and soil permeability and smaller water depth, shear modulus and saturation degree would increase the difference of two coupling algorithms. Meanwhile, the difference between two coupling algorithms is significant around the mono-pile and dumbbell cofferdam, compared with the case without a structure.