Herein, we reported an efficient and universal protocol to prepare gold nanoparticles capped by a dodecanethiol and cetyltrimethyl ammonium bromide interdigitated bilayer which could be dispersed well in either aqueous or organic solvents without additional phase transfer reagents. The gold nanoparticles were synthesized in a micro-emulsion method with transferring the precursor hydrophobic dodecanethiol-capped gold nanoparticles into cetyltrimethyl ammonium bromide aqueous solution. The advantage of this work consists in controlling the diameter of the core gold nanoparticles by capping of dodecanethiol, obtaining high concentration and robust colloidal stability monodisperse amphiphilic gold nanoparticles of various sizes in 2 nm, 5 nm and 7.5 nm, which is very difficult to realize with other methods as far as we known. Very few change existed in the size and intrinsic optical property during the conversion from the aqueous phase to the organic phase and back to aqueous phase, showing these size-controllable amphiphilic gold nanoparticles can be applied not only in biological labeling and sensing, design of diagnostic and therapeutic due to their aqueous soluble biological compatibility, but also in assembling ordered 2D or 3D superlattice due to their monodispersity and high concentration.