Due to pronounced quantum confinement and edge effects, graphene quantum dots (GQDs) demonstrate numerous novel chemical and physical properties and thereby, have potential applications in optoelectronic devices, sensors and biomedical imaging. Doping GQDs with heteroatoms is an effective way to tailor their electronic and optical properties. However, due to different synthesis methods, the widespread use of GQDs doped with heteroatoms has been hindered by the poor understanding of their optical mechanisms. Recently, we studied optical properties of GQDs by employing theoretical calculations and experimental work, which demonstrated that theoretical studies can reveal optical mechanism of GQDs. In this work, the mechanisms underlying the tunable optical properties of GQDs doped with B and S are investigated using density functional theory and time-dependent density functional theory calculations. The electronic structures, optical spectra, molecular orbitals, and electronic density of GQDs are predicted to reveal electron transition processes. Especially, GQDs doped with different B and S patterns are designed to reveal the influence of the existence of O atoms on optical and electronic properties of GQDs. In general, electron-rich S atom increases the HOMO energy, while electron-deficient B atom lowers the LUMO energy, resulting in a decreased HOMO–LUMO gap. Edge doped effect analysis shows that B on GQDs induce a small red shift in absorption spectra whereas a large red shift occurs with surface doped GQDs. However, the absorption spectra of B and O co-doped GQDs exhibit an obvious blue shift and the absorption intensities enhance markedly. For S doped GQDs, the influences of surface and edge doping on absorption spectra of GQDs are almost opposite. Surface doped GQDs induces a small redshift in absorption spectra whereas a large redshift occurs with edge doped GQDs. The recombination of excited, well-separated electron hole pairs can result in enhanced absorption intensity. The heteroatoms doping on the basal plane can transform the sp² hybridized carbon into the sp³ state. It is expected that this work will provide valuable knowledge for understanding and interpreting the electronic and optical properties of GQDs at atomic scale, and give important insights and guidance for the development of methods to controllably synthesize GQDs with well-defined and desirable properties towards specific purposes.