Photovoltaic characteristics of organic solar cells (OSCs) are correlated with microstructural qualities of active layers (ALs). Numerous efforts focused on improving process conditions of ALs to attain effective microstructures to achieve high-efficiency OSCs. Aside from AL process conditions, layer properties under AL can also influence microstructural qualities of AL. In this study, we adopted poly(3-hexylthiophene) (P3HT):(6,6)-phenyl C61-butyric acid methyl ester (PCBM) mixture as AL, poly(3,4-ethylenedioxythiophene):poly(styrene sulfonate) (PEDOT:PSS) as hole extraction layer, and branched polyethyleneimine (BPEI) as electron extraction layer to prepare OSCs with different device structures, that is, normal type (PEDOT:PSS/P3HT:PCBM/BPEI) and inverted type (BPEI/P3HT:PCBM/PEDOT:PSS) structures. We discovered that although devices have similar layer components, they have different photovoltaic characteristics. Inverted devices demonstrated higher power conversion efficiency than normal devices. Various methods, including absorption spectroscopy and microscopy, were used to study AL microstructures of different devices. We observed that P3HT crystallites grown on BPEI had longer vertical size and shorter horizontal size compared with those grown on PEDOT:PSS; these properties could result from larger interfacial tension of P3HT with BPEI than with PEDOT:PSS. Observed shape of P3HT crystallites in inverted devices facilitated efficient charge transport to electrodes and suppressed current leakage. As a result, inverted devices generated improved photovoltaic performance.