A naphthalene diimide (NDI) building block containing hydrazide (H1) and hydroxy (H2) groups self-assembled into a reverse-vesicular structure in methylcyclohexane by orthogonal H-bonding and π-stacking. At an elevated temperature (LCST=43 °C), destruction of the assembled structure owing to selective dissociation of H2–H2 H bonding led to macroscopic precipitation. Further heating resulted in homogeneous redispersion of the sample at 70 °C (UCST) and the formation of a reverse-micellar structure. In the presence of a pyridine (H3)-functionalized pyrene (PY) donor, a supramolecular dyad (NDI–PY) was formed by H2–H3 H-bonding. Slow transformation into an alternate NDI–PY stack occurred by a folding process due to the charge-transfer interaction between NDI and PY. The mixed NDI–PY assembly exhibited a morphology transition from a reverse micelle (with a NDI–PY mixed-stack core) below the LCST to another reverse micelle (with a NDI core) above the UCST via a “denatured” intermediate.