Quantum dots (QDs) are luminescent semiconductor nanomaterials (NMs) with various biomedical applications, but the high toxicity associated with traditional QDs, such as Cd‐based QDs, limits their uses in biomedicine. As such, the development of biocompatible metal‐free QDs has gained extensive research interests. In this study, we synthesized near‐infrared emission Cu, N‐doped carbon dots (CDs) with optimal emission at 640 nm and a fluorescence quantum yield of 27.1% (in N,N‐dimethylformamide [DMF]) by solvothermal method using o‐phenylenediamine and copper acetate monohydrate. We thoroughly characterized the CDs and showed that they were highly fluorescent and stable under different conditions, although in highly acidic (pH = 1–2) or alkaline (pH = 12–13) solutions, a redshift or blueshift of fluorescence emission peak of Cu, N‐doped CDs was also observed. When exposed to human umbilical vein endothelial cells (HUVECs), Cu, N‐doped CDs only significantly induced cytotoxicity at very high concentrations (100 or 200 μg/ml), but their cytotoxicity appeared to be comparable with carbon black (CB) nanoparticles (NPs) at the same mass concentrations. As the mechanisms, 200 μg/ml Cu, N‐doped CDs and CB NPs promoted endoplasmic reticulum (ER) stress proteins IRE1α and chop, leading to increased cleaved caspase 3/pro‐caspase 3 ratio, but CB NPs were more effective. At noncytotoxic concentration (50 μg/ml), Cu, N‐doped CDs successfully labeled HUVECs. In summary, we successfully prepared highly fluorescent and relatively biocompatible CDs to label HUVECs in vitro.