We design a new naphthalenediimide (NDI) π-system, NDI–Fc–NDI, having a ferrocene linker as a hinge unit and long alkyl chains as supramolecular assembling units. The NDI units are “directionally flexible” in concert with the pivoting motion of the ferrocene unit with a small rotational barrier. The NDI units rotate around the ferrocene unit faster than the NMR time scale in solution at room temperature. UV–vis absorption, synchrotron X-ray diffraction, and atomic force microscope studies reveal that NDI–Fc–NDI forms a fibrous supramolecular assembly in solution (methylcyclohexane and highly concentrated chloroform) and film states, wherein the NDI units are in the slipped-stack conformation. The NDI–Fc–NDI supramolecular assembly in the film state exhibits multiple phase transitions associated with conformational changes at different temperatures, which are confirmed by differential scanning calorimetry, polarized optical microscopy, and temperature-dependent X-ray diffraction. Such thermal transitions of NDI–Fc–NDI films also induce changes in the optical and electronic properties as revealed by UV–vis absorption and photoelectron yield spectroscopies, respectively. The thermal behaviors of NDI–Fc–NDI, realized by the unique molecular design, are considerably different from the reference compounds such as an NDI dimer connected with a flexible 1,4-butylene linker. These results provide us with a plausible strategy to propagate the molecular dynamics of the π-system into macroscopic properties in film states; the key factors are (i) the supramolecular alignment of molecular switching units and (ii) the directional motion of the switching units perpendicular to the supramolecular axis.