One dimensional (1-D) nanostructures of conjugated polymers, such as nanofibers, offer the possibility of directed charge transport and improved absorption due to better chains ordering. Poly(3-hexylthiophene) (P3HT) nanofibers can be synthesized by utilizing its interaction with marginal solvents. This work explores the effect of different poor solvents in driving P3HT chain self-assembly into nanofibers and also the effect of a small amount of good solvent in such a poor solvent system in controlling the nanofiber morphology. The organic photovoltaic (OPV) devices based on the blend of P3HT nanofibers and PCBM showed an improved short circuit current when anisole was used compared to p-xylene. Surprisingly, the presence of a small amount of good solvent such as chlorobenzene (CB) in anisole resulted in a higher degree of crystallinity and thinner nanofibers compared to purely anisole system. These are evident from the absorption, scattering and morphology data. The presence of CB delayed crystallization, which is evident from the synchrotron small angle X-ray scattering (SAXS) measurements. This modification of fiber morphology with CB addition into P3HT/anisole results in an improved power conversion efficiency (PCE) of 2.3%; an improvement of more than 50% compared to the pure anisole system. Our investigation provides a new insight into self-assembly of polymers in a mixed solvent system, paving the way to new approaches of controlled self-assembly of organic nanofibers.