We design a new naphthalenediimide (NDI) pi-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 pi-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.