We report the observation of anomalous high photovoltages, which are significantly higher than the energy level offset between the highest occupied molecular orbital (HOMO) of the electron donor (D) and the lowest unoccupied molecular orbital (LUMO) of the acceptor (A), in single trunk shish kebab-like organic p–n junction nanostructures. Creation of such high photovoltages is likely due to the special intermolecular orientation in the unique structure.