Owing to their unique morphology, ultrasmall lateral sizes, and exceptional properties, graphene quantum dots (GQDs) hold great potential in many applications, especially in the fields of electrochemical biosensors, bioimaging, drug delivery, gene delivery, etc. Their biosafety and potential genotoxicity to human and animal cells have been a growing concern in recent years. Especially, the potential DNA damage caused by GQDs is very crucial but still unclear. In this study, the effect of GQDs on DNA damage has been evaluated by a combination of molecular dynamics (MD) simulations and density functional theory. Our results demonstrate that the DNA damaging mechanism of GQDs depends on the size of GQDs. The small GQDs (seven benzene rings) tend to enter into the interior of DNA molecules and cause a DNA base mismatch. The relatively large GQDs (61 benzene rings) tend to adsorb onto the two ends of a DNA molecule and cause DNA unwinding. Due to the strong interaction between guanine (G) and GQDs, the effect of GQDs is much larger on G than on the other three bases (A, C, and T). In addition, the concentration of GQDs could also affect the results of DNA damaging.