Single-crystal silicon is an important semiconductor material. Generally, the surface of single-crystal silicon after ingot slicing is prone to deep surface defects, such as grooves, pits, and cracks, etc. To solve this problem, a two-step laser irradiation method is proposed, which can repair surface defects and decrease surface roughness at the same time. First, the repairable defect depth is forecasted by finite element method (FEM) simulation under different laser parameters. Then, surface defects with various depths can be repaired by using the deeper surface layer melting at a higher energy density of 0.50 J/cm ². However, the thermal capillary flow caused by high energy density can easily lead to the residual high-frequency features on the surface, which will lead to the increase of surface roughness. Subsequently, the residual high frequency features can be effectively eliminated by re-radiating the same surface with a low energy density of 0.20 J/cm ². Finally, the surface with the original surface roughness of 1.057 μm is irradiated by the two-step laser to obtain a defect-free smooth surface with a surface roughness of 26 nm.