A general technique for efficient surface modification of silicon nanocrystals is highly desirable for the development of silicon quantum dots (SiQDs) as fluorescent probes for biological applications. Herein, a facile microwave-assisted hydrosilylation process for the preparation of stable SiQDs in a single step is presented. FTIR spectroscopy indicates that molecules with various terminal functionalities, such as alcohol, alkyl groups, and carboxylic acid, are grafted successfully onto the surface of silicon nanocrystals. The dispersibility of such SiQDs is clearly dependent on the terminal functional groups of the grafted molecules. In addition, the as-prepared SiQDs show excellent cell compatibility, photoluminescence properties, and stability, and their use as long-term intracellular fluorescent probes is also demonstrated. It is envisaged that this facile and effective method for the stabilization and functionalization of SiQDs with tailored wetting and chemical properties will enable wide application of SiQDs in a number of areas.