Chinese medicine is a treasure of the Chinese nation, and charcoal drugs are a class of medicine with distinctive characteristics. Scutellariae Radix Carbonisata (SRC) could be a sort of calcined herb medicate that has been utilized in traditional Chinese medicine (TCM) clinics to treat hypersensitivities. However, to date, the function of the carbonized part and action mechanisms of SRCs have not been elucidated. In this study, novel water-soluble carbon dots (CDs, named SRC-CDs) ranging from 2 to 9 nm were observed and separated from aqueous extracts of SRC. These SRC-CDs were characterized using transmission electron microscopy (TEM) and high-resolution TEM, as well as Fourier transform infrared, ultraviolet-visible, and fluorescence spectroscopy, to determine particle size, morphology, chemical structure, and optical properties. Then, the in vitro antiallergic efficacy of the SRC-CDs was studied in a C48/80-induced RBL-2H3 cell model, in which remarkable antiallergic effects were revealed. These results will provide new solution directions and technical methods for follow-up research of charcoal drugs and new understanding of potential biomedical applications of CDs.