Fluorescent silicon quantum dots (SiQDs) are facilely prepared via one-pot microwave-assisted synthesis. The as-prepared SiQDs feature excellent aqueous dispersibility, robust photo- and pH-stability, strong fluorescence, and favorable biocompatibility. Experiments show the SiQDs are superbly suitable for long-term immunofluorescent cellular imaging. Our results provide a new and invaluable methodology for large-scale synthesis of high-quality SiQDs, which are promising for various optoelectronic and biological applications.