Theoretical and experimental studies suggest that energetic offsets between the charge transport energy levels in different morphological phases of polymer:fullerene bulk heterojunctions may improve charge separation and reduce recombination in polymer solar cells (PSCs). In this work, we use cyclic voltammetry, UV-vis absorption, and ultraviolet photoelectron spectroscopy to characterize hole energy levels in the polymer phases of polymer:fullerene bulk heterojunctions. We observe an energetic offset of up to 150 meV between amorphous and crystalline polymer due to bandgap widening associated primarily with changes in polymer conjugation length. We also observe an energetic offset of up to 350 meV associated with polymer:fullerene intermolecular interactions. The first effect has been widely observed, but the second effect is not always considered despite being larger in magnitude for some systems. These energy level shifts may play a major role in PSC performance and must be thoroughly characterized for a complete understanding of PSC function.