Crystallization and phase segregation during thermal annealing lead to the increase of power-conversion efficiency in poly(3-hexylthiophene) (P3HT):[6,6]-phenyl C61-butyric acid methyl ester (PCBM) bulk-heterojunction solar cells. An understanding of the length and time scale on which crystallization and phase segregation occur is important to improve control of the nanomorphology. Crystallization is monitored by means of grazing incidence X-ray diffraction in real time during thermal annealing. Furthermore, the change in film density is monitored by means of ellipsometry and the evolution of carrier mobilities by means of field effect transistors, both during annealing. From the combination of such measurements with those of device performance as a function of annealing time, it is concluded that the evolution of microstructure involves two important time windows: i) A first one of about 5 minutes duration wherein crystallization of the polymer correlates with a major increase of photocurrent; ii) a second window of about 30 minutes during which the aggregation of PCBM continues, accompanied by an increase in the fill factor.