The influence of micrometer-scale poly(3-hexylthiophene) (P3HT) nanowires (NWs) and P3HT nanocrystals (NCs) on the photocurrent generation in photoactive layers having various thickness values was investigated. Self-organizing P3HT NWs were fabricated using a marginal solvent. Transmission electron microtomography was used to characterize the vertical and horizontal crystalline morphologies of the NWs and their intergrain percolation networks in the active layers. The interpenetrating P3HT NWs promoted charge transport, as demonstrated by the enhanced percolation probability and the reduction in bimolecular recombination. The photovoltaic performances were enhanced as the photoactive layer thickness increased because internal quantum efficiencies of the solar devices prepared with active layers having NWs were maintained with varying thicknesses, suggesting that the conversion of absorbed photons into a photocurrent proceeded efficiently. By contrast, the photovoltaic performances of an NC-only photoactive layer were reduced by the increase in thickness due to its poorly developed percolation pathways. The incorporation of P3HT NWs into the P3HT:indene-C60 bisadduct photoactive layers yielded a device power conversion efficiency (PCE) of 5.42%, and the photocurrent did not decrease significantly up to a thickness of 600 nm, resulting in a PCE of 3.75%, 70% of the maximum PCE of 5.42%.