The morphology of the photoactive layer critically affects the performance of the bulk heterojunction polymer solar cells (PSCs). To control the morphology, we introduced a hydrophobic fluoropolymer polyvinylidene fluoride (PVDF) as nonvolatile additive into the P3HT:PCBM active layer. The effect of PVDF on the surface and the bulk morphology were investigated by atomic force microscope and transmission electron microscopy, respectively. Through the repulsive interactions between the hydrophilic PCBM and the hydrophobic PVDF, much more uniform phase separation with good P3HT crystallinity is formed within the active layer, resulting enhanced light harvesting and improved photovoltaic performance in conventional devices. The PCE of the conventional device can improve from 2.40% to 3.07% with PVDF additive. The PVDF distribution within the active layer was investigated by secondary ion mass spectroscopy, confirming a bottom distribution of PVDF. Therefore, inverted device structure was designed, and the PCE can improve from 2.81% to 3.45% with PVDF additive. Our findings suggest that PVDF is a promising nonvolatile processing additive for high performance polymer solar cells.