We report a two-step phase transfer approach to locate surfactant bilayers on water-soluble luminescent nanocrystals (NCs), through which the surface functionality of the NCs is tunable. Since the species of both inner and outer surfactants of the bilayer are alterable in wide range, the current effort provides a facile approach to anchor various functional groups on aqueous NCs. The primary results indicate that these bilayer-modified NCs are able to be incorporated with various organic and inorganic materials.