O and OH radicals are the most important reactive oxygen species in the plasma treatment of polymer surfaces. In our previous studies, we found that the modification efficiency of polypropylene (PP) surface by O radicals was approximately four times higher than that by OH radicals. This observation contrasts with the well-established fact that the chemical reactivity of O radicals with saturated hydrocarbons (C n H2(n + 1)) is 50–60 times lower than that of OH radicals. In this study, classical molecular dynamics simulations with a reactive force field were used to explain this contradiction. The results showed that the surface modification of PP by O or OH radicals is a Langmuir–Hinshelwood process. Both O and OH radicals penetrated the bulk PP, that is, physical adsorption occurred before the chemical reactions. The penetration depth of O radicals was greater than that of OH radicals. Compared to the case of OH radicals, alkoxy radicals (RO·) are more readily formed upon the interactions of the PP surface with O radicals. Furthermore, the β-scission (splitting of the C–C bonds) of RO· can be accelerated by the physically adsorbed O radicals, leading to earlier breakage of PP chains. The improved efficiency of the surface modification of PP upon exposure to O radicals, in contrast to that of OH radicals, can be attributed to the differences in the above three crucial processes. These findings are significant for modelling and understanding the mechanisms of plasma-polymer surface treatment at the atomic and molecular levels.