Film thickness dependent nanostructure evolution by a post annealing was investigated in poly (3-hexylthiophene):phenyl-C61-butyric acid methyl ester(P3HT:PCBM) films for organic solar cells which were fabricated by dichlorobenzene(DCB) solvent. In case of a 70nm thin film, the thermal annealing process affected to slight increment of the P3HT crystals in the surface region. On the other hand, large number of small sized P3HT crystals near the surface region was formed in the 200nm thick film. The solar cell devices showed the 3% power conversion efficiency(PCE) in 1:0.65 and 1:1 ratio(by weight) of P3HT and PCBM in 70nm and 200nm thickness conditions, respectively. Despite to the similar PCE, the short circuit current Jsc was different in 70nm and 200nm devices, which was related to the different nanostructure of P3HT:PCBM after thermal annealing.