P3DDT (3-dodecylthiophene-2,5-diyl) and PCBM( [6,6]-phenyl C61-butyric acid methyl ester) were fabricated to the active layer of Bulk Heterojunction Organic Solar Cells .We obtained the device efficiency was 0.64 % by evaporating solvent at room temperature. We measured Thermal decomposition Temperature (Td) of P3DDT was 487¢J. But operational temperature was over 90¢J, it could affect the roughness of thin film and make efficiency to be 4¡Ñ10-3(%). For results of experiments, we know that roughness changed by the crystallization of side chain and exciton dissociation modified by the morphology between P3DDT and PCBM. Thin film solar cell has a large effect on the formation of active layer, such as heat treatment, choices of solvents, composition ratio, and speed of spin coating. The efficiency of solar cell has been shown to be highly sensitive to the size, composition and crystallization of the formed domains. We studied two kinds of conjugated polythiophenes with the same main chain but different side chain. When the number of carbon atoms of alkyl side chains is more than 10, some orderly arrangements will occur for side chains between the layers. We tried to explain the crystallization caused by long alkyl side chains determined which intrinsic phenomena are the most evident for altering the PCE of solar cell. After recrystallization, the layered structures of P3DDT can be improved, but those orderly degrees of the arrangements with PCBM are further aggregated. The main point for low PEC and Jsc by heat treatment is the unfavorable and roughened morphology. Charge transfer only occurs at the boundary ,which is interfacial area between donor and acceptor materials, hence, the low Jsc could be caused by poor charge transfer between P3DDT and PCBM. The redistributed arrangement of P3DDT domains exclude PCBM from original space, and it makes PCBM to aggregate large particles, from nanophase to mesophase scales, which reduce mutual solubility to be the source of PCE and Jsc reduction.