The sulfur-selenium doped carbon quantum dots (S,Se-CQDs) were synthesized by one-step through hydrothermal method in this study, which have high fluorescence quantum yield (43%) and advanced ability to scavenge reactive oxygen species (ROS). They were characterized by transmission electron microscope (TEM), nuclear magnetic resonance (NMR), X-ray photoelectron spectroscopy (XPS), fourier transform infrared spectroscopy (FTIR). The results showed that the clearance rate of free radical reached to 40% with 200 μg/mL of S,Se-CQDs. The antioxidant activity of S,Se-CQDs is related to -SH and Se-SH on carbon quantum dots. S,Se-CQDs were able to access to cells which is beneficial to enhance the removal efficiency to ROS. In the biocompatibility experiment, the cell survival rate exceeded 95%, there was little effect on hatching rate, survival rate and heart rate of zebrafish which demonstrated that S,Se-CQDs have an excellent biocompatibility. It prompts that S,Se-CQDs will has proud application prospects in the field of biomedicine.