Here, we demonstrate the correlation between the surface roughness of the ZnO interlayer used as an electron transporting interlayer (ETL) in organic inverted solar cells (ISCs) and the photovoltaic performance of the ISCs. Three different surfaces of the ZnO ETL are studied in ISCs with the polymer poly[2,3-bis-(3-octyloxyphenyl)quinoxaline-5,8-diyl-alt-thiophene-2,5-diyl] (TQ1) mixed with [6,6]-phenyl C71 butyric acid methyl ester (PC71BM) as the active layer. The results obtained from these ISCs show that power conversion efficiency increases from 2.7% to 3.9% when the root-mean-square roughness of the ZnO layer decreases from 48 to 1.9 nm. Moreover, it is found that the short-circuit current density is higher in the ISC based on the smoother ZnO interlayer, with a larger donor/acceptor (D/A) interfacial area in the active layer that facilitates exciton dissociation. The reduced effective interfacial area between the photoactive layer and the ZnO interlayer with decreased ZnO surface roughness leads to an observed improvement in both fill factor and open-circuit voltage, which is ascribed to a reduced concentration of traps at the interface between the ZnO interlayer and the active layer.