Flake-like Al-doped ZnO (AZO) nanostructures including dense AZO nanorods were obtained via a low-temperature (100°C) hydrothermal process. By doping and varying Al concentrations, the electrical conductivity (σ) and morphology of the AZO nanostructures can be readily controlled. The effect of σ and morphology of the AZO nanostructures on the performance of the inverted organic solar cells (IOSCs) was studied. It presents that the optimized power conversion efficiency of the AZO-based IOSCs is improved by approximately 58.7% compared with that of un-doped ZnO-based IOSCs. This is attributed to that the flake-like AZO nanostructures of high σ and tunable morphology not only provide a high-conduction pathway to facilitate electron transport but also lead to a large interfacial area for exciton dissociation and charge collection by electrodes.