Here, we report a simple method to control the location of nanoparticles in colloidal block-copolymer assemblies by using nanoparticles modified with mixed surface ligands. The binary self-assembly of amphiphilic polymers of polystyrene-b-poly(acrylic acid) (PS-b-PAA) and gold nanoparticles (AuNPs) modified with a hydrophobic ligand, dodecanethiol (DT), led to polymer micelles with nanoparticles segregated in the core of polymer micelles. On the other hand, AuNPs modified with mixed ligands of mercaptoundecanol (MUL) and DT were distributed at the PS-PAA interface, reducing the interfacial energy between the two polymers. This result was in good agreement with the prediction by the surface energy calculations. We also showed that the AuNPs with mixed ligands can decorate preformed polymer assemblies by the interfacial self-assembly. Furthermore, we demonstrated the compartmentalization of two different types of nanoparticles in colloidal polymer assemblies based on the strategy.