Delicate control over architectures via crystallization-driven self-assembly (CDSA) in aqueous solution, particularly combined with external stimuli, is rare and challenging. Here, we report a stepwise CDSA process thermally initiated from amphiphilic poly(N-allylglycine)-b-poly(N-octylglycine) (PNAG-b-PNOG) conjugated with thiol-terminated triethylene glycol monomethyl ethers ((PNAG-g-EG3)-b-PNOG) in aqueous solution. The diblock copolymers show a reversible thermoresponsive behavior with nearly identical cloud points in both heating and cooling runs. In contrast, the morphology transition of the assemblies is irreversible upon a heating–cooling cycle because of the presence of a confined domain arising from crystalline PNOG, which allows for the achievement of different nanostructured assemblies by the same polymer. We demonstrated that the thermoresponsive property of PNAG-g-EG3 initiates assembly kinetically that is subsequently promoted by crystallization of PNOG thermodynamically. The irreversible morphology transition behavior provides a convenient platform for comparing the cellular uptake efficiency of nanostructured assemblies with various morphologies that are otherwise similar.