A new conjugated polymer based on S,7-bis(2-ethylhexyl)benzo[1,2-c:4,5-c']dithiophene-4,8-dione, named as PBDTBDD, was designed, synthesized, and applied in polymer solar cells (PSCs). A power conversion efficiency (PCE) of 6.67% was obtained from the PBDTBDD/PC61BM-based PSC, which is a remarkable result for the PSCs using PC61BM as electron acceptor. The PBDTBDD/PC61BM-based device exhibits a narrow absorption band and excellent quantum efficiency in the range from 500 to 700 nm. Furthermore, PBDTBDD shows a strong aggregation effect in solution state, and the study indicates that although the temperature used in solution preparation has little influence on molecular orientation as well as crystallinity of the D/A blend, it plays an important role in forming proper domain size in the blend. This work provides a good example to reveal the correlation between the morphology of the blend films and the processing temperature of the solution preparation. Furthermore, the study in this work suggests an interesting and feasible approach to modulate domain size without changing crystallinity of the blend films in PSCs.