Cylindrical structures are widely employed in the offshore engineering. How to protect the structures in real sea environment is a vital issue for scientists and engineers. In this paper, the interaction of short-crested waves with a concentric surface-piercing two-cylinder system is studied based on linear wave theory using the scaled boundary finite-element method (SBFEM), a novel semi-analytical method with the advantages of combining the finite-element method (FEM) with the boundary-element method (BEM). The interior cylinder is impermeable and the exterior cylinder is thin and porous to protect the interior cylinder. Both of cylinders are bottom mounted. Wave elevation in the annular region is found dependent on the short-crested phase, and the total forces fluctuate as the phase changes. It is further revealed that the maximum total forces are smaller than those induced by plane waves and standing waves with the same total wave number.