A simple chemical-etching approach is used to prepare the silicon carbide quantum dots (QDs). The raw materials of silicon carbide (SiC) with homogeneous nanoparticles fabricated via self-propagating combustion synthesis are corroded in mixture etchants of nitric and hydrofluoric acid. After sonication and chromatography in the ultra-gravity field for the etched products, aqueous solution with QDs can be obtained. The microstructure evolution of raw particles and optical properties of QDs were measured. Different organophilic groups on the surface like carboxyl, oxygroup, and hyfroxy were produced in the process of etching. Fluorescent labeling and imaging for living cells of Aureobasidium pulluans were investigated. The results indicated that SiC QDs were not cytotoxic and could stably label due to the conjugation between organophilic groups of QDs and specific protein of cells, it can be utilized for fluorescent imaging and tracking cells with in vivo and long-term-distance. Moreover, mechanism and specificity of mark were also analyzed.