The effect of the Stone-Wales (SW) defect on the energetic, structural, electronic properties of Na/Na+ adsorption on the Hexa-peri-hexabenzocoronene (HBC) nanographene is investigated using density functional theory calculations. We showed that two kinds of SW defects can be generated in the structure of HBC, and the defected sheets are less stable than the intrinsic HBC by about 63.2–65.3 kcal/mol. The heptagonal ring of SW defect is the most favorable site for the Na and Na+ adsorption and the adsorption energies increase from −0.8 and −33.2 kcal/mol on the intrinsic HBC to −16.7 and −39.3 kcal/mol on the SW-HBC, respectively. The predicted energy barrier for an Na atom to move from a heptagonal ring to another one in the SW-HBC is about 4.9 kcal/mol, indicating a high ion mobility compared to the pristine HBC. The SW defect increases the Na diffusion coefficient from 3.46 × 10−11 to 2.83 × 10−6 cm2/s. Although the SW defect increases the ion mobility, it has an undesirable effect on the cell voltage, if a HBC nanographene is used in the anode of Na-ion batteries.