A new method for encapsulating nanomaterials within intermediary layer cross-linked (ILCL) polymeric micelles using a bifunctional photo-cross-linking agent was developed. For ILCL polymeric micelles, an amphiphilic triblock copolymer of poly(ethylene glycol)-b-poly(2-hydroxyethyl methacrylate)-b-poly(methyl methacrylate) (PEG-PHEMA-PMMA) was synthesized via consecutive atom transfer radical polymerization (ATRP), Di(4-hydroxyl benzophenone) dodecanedioate (BPD) was used as a bifunctional photo-cross-linking agent. The PMMA-tethered Au nanoparticles and BPD, or pyrene and BPD were encapsulated in the PEG-PHEMA-PMMA micelles, and their intermediary layers were photo-cross-linked by UV irradiation for 1 h. The HEMA units donated labile hydrogens to the excited-state benzophenone groups in BPD, and they were subsequently cross-linked by BPD through radical-radical combination. The spherical structures of the PEG-PHEMA-PMMA micelles containing the Au nanoparticles or pyrene were unaffected by the photo-cross-linking process.