Various pathways have been utilized to manipulate microphase separation (MPS) of block copolymers, but the obtained MPS nanostructures are often suffering from poor thermal stability. Here, confined self-assembly is first adopted to thermally stabilize and conveniently pattern the MPS morphologies of an amphiphilic liquid-crystalline block copolymer (LCBC) composed of hydrophilic poly(ethylene oxide) (PEO) and hydrophobic azobenzene-containing polymethacrylate. The MPS nanostructures are thermally stabilized by top coating a layer of water-soluble polymer, sodium polystyrenesulfonate (PSSNa), as a result of coordination interaction between PEO and PSSNa. Interestingly, both thermal annealing and rubbing-treated polyimide film caused reorientation of mesogens in the PSSNa-coated LCBC film; however, the orientation of PEO nanocylinders remained unchangeable. This indicates that the PEO nanocylinders are selectively anchored by the PSSNa covering layer, regardless of the changes of mesogenic orientation. Thus, complicated hierarchical nanostructures can be fabricated effortlessly and preserved nondestructively by selected-area confined self-assembly or noncontact photopatterned technology due to the existence of photoresponsive azobenzene moieties.