In this study, we quantitatively investigated the temperature-dependent phase transition behaviors in thin films of an interesting semirod-coil diblock copolymer, poly(styrene)-b-poly(oligothiophene side chain modified isoprene) (PS-b-POTI), and the resulting morphological structures using synchrotron grazing incidence X-ray scattering combined with differential scanning calorimetry. These analyses provided detailed information about the morphologies of the phase-separated domains and the molecular structures formed in each domain. At room temperature, the diblock copolymer molecules in thin films were found to form an alternately stacked structure comprised of amorphous PS and smectic-A POTI microdomains whose stacking direction is parallel to the film plane. On heating, the films underwent a phase transformation to a hexagonal cylinder structure with cylindrical POTI domains in the PS matrix oriented normal to the film plane. This phase conversion is induced by the transformation of the POTI domains from a smectic-A phase to an isotropic phase, where the smectic-A phase is composed of a laterally ordered structure of interdigitated bristles in the POTI blocks. On the basis of these structural analysis results, we propose models for the molecular structures of the diblock polymer thin films at various temperatures.