Non-doped and chemically p-doped poly(3-hexylthiophene) (P3HT) nanowires are investigated by optical spectroscopy and atomic force microscopy (AFM) to reveal the effects of doping on their aggregation processes and nanoscale morphologies. The AFM studies on the non-doped P3HT nanowires formed in the early aggregation stage demonstrate that P3HT molecules will probably go through either packing of high-aspect ratio multi-chain/single-chain aggregates or packing of solubilized individual chains depending on experimental conditions. High-resolution AFM images also show the connecting segments between ordered domains of P3HT. For pdoping of P3HT in the solution phase, the addition of 7,7,8,8-tetracyano-2,3,5,6-tetrafluoroquinodimethane (F 4 -TCNQ), a p-dopant, will greatly accelerate the aggregation rate of 1D P3HT nanostructures. The doped P3HT nanowires are comprised of linearly connected domains that are 40− 60 nm wide and 5−10 nm high. Compared with the non-doped P3HT nanowires, doped nanowires show smoother edges and less protruding segments, likely due to a different aggregation mechanism. Furthermore, the doped nanowires tend to agglomerate into disordered bundles and clusters because of the presence of F 4 -TCNQ counterions and complexity resulting from Coulomb interactions and other doping-induced growth defects.