Self-assembled block copolymer (BCP) thin films and their nanocomposites provide nanostructures useful in myriad applications. While conventional characterization techniques provide an understanding of film surface and internal structures, optical super-resolution microscopy (OSRM) has recently emerged as an alternative way to characterize nanoscopic polymer morphology. This work describes self-assembled poly(isoprene)-block-poly(styrene)-block-poly(N,N-dimethylaminoethyl methacrylate) (PI-b-PSb-PDMAEMA or ISA) triblock terpolymer thin films with all three blocks exposed at the top surface. Structural characterization of neat films with standard techniques, including grazing-incidence small-angle X-ray scattering (GISAXS), atomic force microscopy (AFM), and electron microscopy (EM), reveals a co-continuous network in the substructure of the films and hexagonally ordered top surface structures. Nanocomposite thin films incorporating two chemically and optically orthogonal core−shell optical nanoparticle probes by simple physical mixing and evaporation-induced self-assembly (EISA) retain this morphology while enabling two-color OSRM imaging of different BCP nanodomains. This approach suggests that fine-tuned organic ligand shells enable labeling of different blocks based on shell polarity, demonstrating a straightforward pathway to multicolor OSRM characterization of chemically distinct nanodomains.