Atomic oxygen (AO) is one of the dominant components of the residual atmosphere in low Earth orbit. AO collides with spacecraft with a translational energy of 5 eV, forming nanoscale protrusions on polymeric materials. To clarify the influences of a polymer's chemical structure on the formation of AO-induced microstructures, this study investigated the size of free-volume holes and the layer thickness that interacted with AO for polyethylene (PE), polypropylene (PP), and polystyrene (PS) by positron annihilation lifetime spectroscopy. The injection energies of positrons varied from 1.3 to 10 keV to adjust the injection depth (range) into the polymers (40 nm-1.6 μm). For the pristine films, the lifetime of ortho-positronium (o-Ps, τ3) was longer in the order of PS, PP, and PE regardless of the injection energy of positrons, showing the different sizes of free-volume holes with radii of 0.29, 0.31, and 0.32 nm, respectively. The fraction of the decay component corresponding to o-Ps in all decay components (relative intensity of o-Ps, I3) was used to investigate the chemical change induced by AO exposure. The I3 values for the three polymers were decreased by AO exposure of (2-5) × 1018 atoms/cm2 or more at a depth of 40-48 nm, obtained by 1.3 keV positrons. This indicates that AO formed polar groups (i.e., an oxidized layer) on the polymer surfaces. The maximum depths of such chemical change for PE and PP were deeper than that for PS. The different sizes of free-volume holes would affect the diffusion or ballistic penetration of AO, resulting in the difference in the oxidized layers' thicknesses and surface morphologies.