Nitrogen-doped graphene quantum dots (N-GQDs) are promising biocompatible nanomaterial which has received much attention for biological application. However, the effect of the engineered electronic structure of N-GQDs to the fluorescence of GQDs applied for bio-imaging is still under debate. In this study, N-GQDs were synthesized by a facile one-step hydrothermal method for 10 hours at 180°C and theoretical calculation of electronic structure using density functional theory (DFT) by GAUSSIAN 09, were compared. Single to multilayer of N-GQDs with the particle size of 3.2 nm in average were obtained from hydrothermal synthesis. The optical properties of N-GQDs emitted green photoluminescence (PL) at 525 nm (2.36 eV) with PL excitation (PLE) at 367 nm (3.38 eV). From DFT calculation, the optoelectronic properties of GQDs from HOMO to LUMO differ between edge functionalization and graphitic nitrogen doping. Furthermore, cells cytotoxity showed that N-GQDs possess non-toxic property, and the cells were presented with high viability. In summary, by comparing experimental and theoretical calculations, the electronic properties of N-GQDs could enhance their reactivity in photo-electronics for biological application.