Abstract: Thin silicon (Si) wafers with different thicknesses can be obtained using Smart-Cut technology. Doping elements in the silicon raw material may affect the structure and performance of the Smart-Cut Si wafers. Phosphorus is a commonly used doping element in silicon wafers. It is thus meaningful to study the effects of phosphorus doping on surface modification and defect evolution in the Smart-Cut Si. However, there is a lack of systematic research on the effect of phosphorus doping on the surface exfoliation behavior of silicon wafers. Therefore, in this paper, single crystal silicon samples with the intrinsic and three phosphorus doping concentrations were implanted with 1.5 MeV H⁺ at room temperature, and subsequently annealed at 300 °C and 550 °C. The effects of phosphorus doping on surface exfoliation were investigated by scanning electron microscopy, non-contact optical profilometry, and Raman spectroscopy. Lightly phosphorus doping leads to the appearance of ridge-like structures, while heavily phosphorus doping leads to the appearance of pit-like structures on the substrate surface of the samples. Moreover, the roughness of the substrate surface and the percentage of the special structures decrease with increasing phosphorus concentration. The thermal annealing and the phosphorus doping both affect the distribution of damaged layer in the implantation area. This study discusses the effects of phosphorus-hydrogen repulsion on hydrogen implantation-induced defect formation and annealing evolution behavior, as well as the influence of defect evolution on surface morphology changes.