Accurately analyzing wave–structure interactions is crucial for the design and operational safety of ships and marine structures. This paper presents a fully nonlinear potential-flow approach for simulating wave–structure interactions using the newly proposed spectral coupled boundary element method (SCBEM). The SCBEM efficiently models an extensive water body that encompasses structures by establishing a boundary element method (BEM) computational domain solely around the object of interest while accurately simulating the far-field broad water by a spectral layer. To further improve efficiency, graphics processing unit acceleration is hired during iterative solving of the boundary value problem in the already small-sized interior BEM domain. Simulations are conducted to validate the accuracy of the method on cases with strong nonlinear phenomena, including wave run-up on a single cylinder, diffraction of a four-cylinder array, near-trapped modes for closely spaced columns, and gap resonance that occurred in side-by-side offloading. The wave run-up, diffraction wave pattern, near-trapped mode, and gap resonance frequency obtained by the proposed method are in good agreement with data from experiments and published literature. The quite good accuracy and the exceptional computational efficiency of the SCBEM demonstrate its promising potential for more application in practical marine problems.