In this paper, hydrothermal method has been employed to synthesize oxygen-modified carbon dots (O-CDs) from citric acid and nitrogen and sulfur modified carbon dots (N,S-CDs) from citric acid and cysteine. Both as-prepared carbon dots achieve naked-eye observable blue-green luminescence. Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS) are used to exhibit the chemical composition of carbon dots. The structure and size of both carbon dots are similar via transmission electron microscopy (TEM) and dynamic light scattering (DLS), which indicates that the function of size effect can be neglected in this study. Fluorescence properties, UV-vis absorption and solubility are systemically studied to investigate the influence of surface modification. The N,S-CDs show high quantum yield and excitation independent photoluminescence, however, the O-CDs present low quantum yield and excitation dependent photoluminescence, and both carbon dots achieve strong photo-stability. The cytotoxicity of carbon dots is also performed on U87-MG brain tumor cells, which shows that both carbon dots process good biocompatibility and low toxicity in live cell. The bright cellular imaging photos indicate that both carbon dots have great potential to serve as high quality optical imaging probes.