Wave-structure interaction exists widely in the field of ocean engineering. Current numerical simulations on wave -structure interaction are usually limited to two dimensions. However, in many practical engineering problems, the three-dimensional effect is so significant that a two-dimensional simulation cannot accurately reflect the real hydrodynamic characteristics of offshore structures. On the basis of the smoothed particle hydrodynamics (SPH) method, three cases, i. e., double-submerged breakwaters, an oscillating wave surge converter, and a floating body, are simulated in this study in two-dimensional, quasi-two-dimensional, and three-dimensional conditions, respectively. The flume width effect on the hydrodynamic characteristics of the structure is discussed to explore the three-dimensional effect. Graphics processing unit (GPU) accelerated technology is applied in the present simulations to improve computational efficiency. The numerical results show that the three-dimensional effect of wave-structure interaction may cause a complex eddy current structure, which can reduce the effect of structures on wave propagation, enhance the effect of waves on structures, and strengthen the complexity of the structure motion.