The attractive optoelectronic properties of conducting polymers depend sensitively upon intra- and inter-polymer chain interactions, and therefore new methods to manipulate these interactions are continually being pursued. Here, we report a study of the isotopic effects of deuterium substitution on the structure, morphology and optoelectronic properties of regioregular poly(3-hexylthiophene)s with an approach that combines the synthesis of deuterated materials, optoelectronic properties measurements, theoretical simulation and neutron scattering. Selective substitutions of deuterium on the backbone or side-chains of poly(3-hexylthiophene)s result in distinct optoelectronic responses in poly(3-hexylthiophene)/[6,6]-phenyl-C61-butyric acid methyl ester (PCBM) photovoltaics. Specifically, the weak non-covalent intermolecular interactions induced by the main-chain deuteration are shown to change the film crystallinity and morphology of the active layer, consequently reducing the short-circuit current. However, side-chain deuteration does not significantly modify the film morphology but causes a decreased electronic coupling, the formation of a charge transfer state, and increased electron-phonon coupling, leading to a remarkable reduction in the open circuit voltage.