Fluorination is a promising modification method to adjust the photophysical profiles of organic semiconductors. Notably, the fluorine modification on donor or acceptor materials could impact the molecular interaction, which is strongly related to the morphology of bulk heterojunction (BHJ) blends and the resultant device performance. Therefore, it is essential to investigate how the molecular interaction affects the morphology of BHJ films. In this study, a new fluorinated polymer PBDB-PSF is synthesized to investigate the molecular interaction in both nonfluorinated (ITIC) and fluorinated (IT-4F) systems. The results reveal that the F-F interaction in the PBDB-PSF:IT-4F system could effectively induce the crystallization of IT-4F while retaining the ideal phase separation scale, resulting in outstanding charge transport. On the contrary, poor morphology can be observed in the PBDB-PSF:ITIC system because of the unbalanced molecular interaction. As a consequence, the PBDB-PSF:IT-4F device delivers an excellent power conversion efficiency of 13.63%, which greatly exceeds that of the PBDB-PSF:ITIC device (9.84%). These results highlight manipulating the micromorphology with regard to molecular interaction.