This manuscript describes how to design and fabricate efficient inverted solar cells, which are based on a two-dimensional conjugated small molecule (SMPV1) and [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM), by utilizing ZnO nanorods (NRs) grown on a high quality Al-doped ZnO (AZO) seed layer. The inverted SMPV1:PC71BM solar cells with ZnO NRs that grew on both a sputtered and sol-gel processed AZO seed layer are fabricated. Compared with the AZO thin film prepared by the sol-gel method, the sputtered AZO thin film exhibits better crystallization and lower surface roughness, according to X-ray diffraction (XRD) and atomic force microscope (AFM) measurements. The orientation of the ZnO NRs grown on a sputtered AZO seed layer shows better vertical alignment, which is beneficial for the deposition of the subsequent active layer, forming better surface morphologies. Generally, the surface morphology of the active layer mainly dominates the fill factor (FF) of the devices. Consequently, the well-aligned ZnO NRs can be used to improve the carrier collection of the active layer and to increase the FF of the solar cells. Moreover, as an anti-reflection structure, it can also be utilized to enhance the light harvesting of the absorption layer, with the power conversion efficiency (PCE) of solar cells reaching 6.01%, higher than the sol-gel based solar cells with an efficiency of 4.74%.