Poly(3-hexylthiophene) (P3HT) thin films are spin casted with thickness ∼ 300 nm. Thin films are irradiated at different fluences from 1 × 109 ions/cm2 to 1 × 1011 ions/cm2 by 90 MeV Ni+7 ion beam. The molecular ordering of P3HT is explained in terms of less heating effects in the halo region surrounding the incident ion path. The increased conductivity has been observed due to increased conjugation length and molecular ordering. Variation in the absorption and emission spectra due to energetic ions is also investigated.