The influence of annealing temperature on the structural and electrical properties of conjugated poly(dodecyl-quaterthiophene) (PQT-12) polymer films is exploited. The temperature induced changes of structural parameters are monitored by in situ grazing incident X-ray diffraction (GIXD) and the conductivity. They are complemented by studies of the dielectric properties using variable angle spectroscopic ellipsometry (VASE). An increase of the scattered intensity, the size of the crystalline domains, and the current response is observed for a first thermal cycle with stepwise heating up to 90 degrees C, which revealed two polymorphs with different degrees of interdigitation in PQT-12. Irreversible changes are observed for the second cycle with a higher thermal budget up to 140 degrees C and are connected with a transition from the highly ordered to powder-like disordered phase for the main PQT-12 form whereas the second polymorph with stronger interdigitation completely vanished. In agreement with these observations high-temperature VASE studies demonstrated a blue shift of the transitions with a reduction in the conjugation length caused by an increase in the twist and torsion of the backbone. Combined GIRD, VASE, and electrical characterizations show that PQT-12 exhibits a complex interplay between two polymorphs with a strong influence on the charge carrier transport depending on the thermal budget employed.