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Thermal annealing represents an important stage for the fabrication of active layers for organic solar cells. The crystalline organization improves charge carrier mobility and induces the proper morphology of the electron donor and electron acceptor. In this work, the optimal annealing time for maximization of crystalline volume fraction and the crystallization mechanisms of conjugated polymer films synthesized in our group for solar cell application has been determined by grazing incidence wide-angle X-ray scattering (GIWAXS). By following the evolution of the diffraction peak position, the peak area, and the full width at half maximum (FWHM), it was possible to determine the proper annealing time and to identify the stages corresponding to crystallites formation and growth for poly(butyl octyl benzodithiophene-co-benzothiadiazole) (PBOBDTBTD), poly(butyl octyl benzodithiophene-co-thiophene) (PBOBDTTh), and two different poly(3-hexylthiophene), one of lower molar mass synthesized through Kumada mechanism (P3HTA) and other of higher molar mass through Grimm mechanism (P3HTB). The results show that annealing time increases with polymer backbone rigidity, around 1200 s, 800 s, and 400 s for PBOBDTBTD, PBOBDTTh, and P3HT, respectively. Thus, crystallization in PBOBDTBTD and P3HT mainly occurs through several stages of crystallite formation. In contrast, crystallite growth is significant in PBOBDTTh, promoted both by the flexibility of the polymer chain and the symmetry of the structural unit position in the backbone. For all polymers, an unexpected increase of interplanar distance during crystallites formation and growth has been detected. We attribute this behavior to the confinement of the chains in thin films, which may inhibit the interdigitation effect usually observed in bulk polymer and associated with increased packing between side chains, diminishing the average distance among conjugated backbones.