The development of ultrastable and highly fluorescent heteroatoms-doped graphene quantum dots (GQDs) for bioimaging remains a challenge due to the fluorescence quenching caused by binding between the heteroatoms-based functional groups of the GQDs and common metal ions in biological systems. Here, we developed a facile hydrothermal method to prepare nitrogen−sulfur doped GQDs (NS-GQDs). The fluorescence signals of the NS-GQDs are highly stable in the existence of different metal ions. Two natural products, aspartic acid and cysteine, were utilized as the carbon precursors and heteroatomic (nitrogen and sulfur) sources. The produced NS-GQDs showed a quantum yield up to 19.3 ± 1.7% with a maximum emission of 480 nm under the excitation of 400 nm. The elemental analysis, including X-ray photoelectron spectroscopy (XPS) and energy dispersive spectroscopy (EDS), and Fourier-transform infrared spectroscopy (FTIR), were performed to characterize the composition and surface groups of NS-GQDs. Additionally, the NS-GQDs not only showed notable photostability, but also thermostability and chemical stability. Moreover, the NS-GQDs demonstrated very low cellular cytotoxicity in vitro. Finally, the NS-GQDs were applied for fluorescence imaging of cells, which also exhibited excellent fluorescent stability even with treatment of copper ions. The results indicated that the developed novel NS-GQDs have a promising potential to be used as ultrastable fluorescent agent in the field of bioimaging and biosensing.