Two-step phase transfer using C18AA molecules as the transfer agent was found to be very useful for the fractionation of large Au nanoparticles (NPs) (average diameter 7.7 nm), small Au NPs (average diameter 4.9 nm), and Au nanowires (NWs) according to their surface structural distinction. We also demonstrated that the use of organic solvents with different solubilities for C18AA was effective for the fractionation of Au nanocrystals.