While regulation of the nanoscale microstructure of the active layers in organic bulk heterojunction (BHJ) solar cells, particularly for conjugated polymer–fullerene blend systems, has been shown to be highly important when maximizing power conversion efficiency, little is known about the role of disordered polymer chains in the photovoltaic (PV) behaviors and electrochemical potential drops of polymer–fullerene interfaces. In this study, the microstructural-dependent PV properties of a series of poly(3-hexylthiophene) (P3HT):fullerene (i.e., [6,6]-phenyl-C61-butyric acid methyl ester, or PCBM) blending films with different compositions have been investigated using several experiments (i.e., absorption spectroscopy, Raman spectroscopy, X-ray diffraction, and atomic force microscopy) and theoretical methods (i.e., spectroscopic simulation and quantum mechanical calculations). A strong correlation exists between amorphous P3HT chain properties, characterized by degree of conjugation (L eff), and PV parameters. The impact of L eff of amorphous P3HT on exciton dissociation is addressed, thus providing an ideal structural model for organic BHJ solar cells. Although bigger P3HT and PCBM domains favor carrier transport, the control of disordered P3HT segments and PCBM contact is crucial to exciton dissociation, which can consequently optimize PV performance.