In this study, diamino moiety functionalized silica nanoparticles with the size of 118 ± 12 nm were successfully synthesized and directly introduced into a chiral capillary electrophoresis system to improve the enantioseparation of 9-fluorenyl methoxycarbonyl derivatized amino acids using norvancomycin as chiral selector. Under acidic background electrolyte conditions, functional silica nanoparticles can be readily adsorbed onto the inner surface of bare silica capillary column through electrostatic interaction to form a dynamic coating, resulting in a reversed anodic electro-osmotic flow (i.e. from cathode to anode). As expected, chiral amino acid derivatives (usually negatively charged) can be rapidly separated under co-electro-osmotic flow conditions in the current separation system. Furthermore, the column performance and detection sensitivity for the enantioseparation were also obviously improved because the adsorption of chiral selector of norvancomycin to the capillary wall was greatly suppressed. Some important factors influencing the separation, such as the coating thickness, background electrolyte concentration, functional silica nanoparticles concentration, and the organic modifier were also investigated and the optimized separation conditions were obtained.