This work presents the synthesis and self-organization of the calamitic fluorinated mesogen, 1,1,2,2-tetrafluoro-2-(1,1,2,2-tetrafluoro-4-iodobutoxy)ethanesulfonic acid, a potential model for perfluorosulfonic acid membranes (PFSA). The compound is derived in three steps from 1,1,2,2-tetrafluoro-2-(1,1,2,2-tetrafluoro-2-iodoethoxy)ethanesulfonyl fluoride, achieving an 78% overall yield. The resulting compound exhibits intricate thermal behavior. At 150 °C, a crystal-to-crystal transition is observed due to the partial disordering of calamitic molecules, which is followed by isotropization at 218 °C. Upon cooling, sample ordering occurs through the formation of large smectic liquid crystalline phase domains. This thermotropic state transforms into a layered crystal phase at lower temperatures, characterized by alternating hydrophilic and hydrophobic layers. Using X-ray diffraction, crystalline unit cell models at both room temperature and 170 °C were proposed. Computer simulations of the molecule across varying temperatures support the idea that thermal transitions correlate with a loss of molecular orientation. Importantly, the study underscores the pivotal role of precursor self-organization in aligning channels during membrane fabrication, ensuring controlled and oriented positioning.