Two DSC exotherms for cis-trans thermal isomerization of polyacetylene (PA) films were found near 145 and 170 degrees C. These exotherms are related to the higher-order structure of PA films, depending on the sample preparation conditions. The high-temperature peak corresponds to ordered crystallites (A state), which is prominent in conventional Shirakawa polyacetylene (S-PA) and moderately stretchable PA (ms-PA) films. The low-temperature peak corresponds to disordered crystallites (B-state) found in highly stretchable PA (hs-x) films. The distribution of crystalline order in the B state depends on the materials. The A state is transformed to B state upon stretching of ms-PA, but the B state is not transformed to A state by stretching. The supermolecular structure is discussed.