The in situ morphology change upon thermal annealing in bulk heterojunction blend films of regioregular poly(3-hexylthiophene) (P3HT) and 1-(3-methoxycarbonyl)-propyl-1-phenyl-(6,6)C61 (PCBM) is measured by a grazing incidence X-ray diffraction (GIXD) method using a synchrotron radiation source. The results show that the film morphology—including the size and population of P3HT crystallites—abruptly changes at 140 °C between 5 and 30 min and is then stable up to 120 min. This trend is almost in good agreement with the performance change of polymer solar cells fabricated under the same conditions. The certain morphology change after 5 min annealing at 140 °C is assigned to the on-going thermal transition of P3HT molecules in the presence of PCBM transition. Field-emission scanning electron microscopy measurements show that the crack-like surface of blend films becomes smaller after a very short annealing time, but does not change further with increasing annealing time. These findings indicate that the stability of P3HT:PCBM solar cells cannot be secured by short-time annealing owing to the unsettled morphology, even though the resulting efficiency is high.