Here, we report on the hydrophobic interaction-mediated direct self-assembly of amphiphilic ‘nanocrystallo-polymers', hydrophilic poly(amino acid) derivatives grafted with hydrophobic Au nanocrystals. Au nacnocrystals protected by an alkyl chain monolayer are chemically conjugated onto a hydrophilic polymer backbone via a thiolate bond and these amphiphiles can direct the self-assembly into forming spherical aggregates by serving as the hydrophobic component in a nanocrystallo-polymer system. With the selective introduction of a dodecyl chain as the co-hydrophobic component, we can obtain a wide range of hydrophilic/hydrophobic compositions of nanocrystallo-polymers with multiple morphologies, i.e. spherical aggregates, core-shell unimolecular micelles, and cylinders, in aqueous solutions. The present study has a number of advantages over previous methods. Since conjugated nanocrystals are the hydrophobic component of amphiphiles, they have dynamic self-assembling and surface-active properties. Therefore, the self-assembling process is simple, diverse morphologies can be obtained, and the arrangement of nanocrystals is more regular and controllable.