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IR and Raman spectroscopy investigations are carried out on single crystals of the organic semiconductor 7-decyl-2-phenyl[1]benzothieno[3,2-b][1]benzothiophene (Ph-BTBT-10) subjected to thermal cycling through the boundaries of its Smectic E (SmE) and Smectic A liquid crystal phases, gaining insight on their structural order. IR measurements in polarized light provide a precise description of both the orientational order of the molecule BTBT’s rigid cores and the conformational status of its substituents in the mesophases and shed light on the processes occurring at the phase transitions. The Raman mapping of the crystals obtained in the reverse SmE-to-crystal transition reveals the presence of a distinctive polycrystallinity pattern in the recovered samples, an effect which may contribute to the understanding of the variation of the charge carrier mobility of devices experiencing thermal annealing processes.