The modifications of Poly(3-Hexylthiophene) (P3HT) thin films have been investigated by irradiating with 90 MeV Ni7+ ions at different fluences (1 × 109 to 1 × 1011 ions/cm2). Thin films have been characterized by micro-Raman Spectroscopy, Fourier Transform Infrared Spectroscopy (FTIR), X-ray Diffraction (XRD), X-ray Photoelectron Spectroscopy (XPS), UV-visible absorption Spectroscopy, Photoluminescence spectroscopy (PL), Atomic Force Microscopy (AFM) and small angle X-ray scattering (SAXS) analysis. The narrow FWHM of C=C mode and the larger intensity ratio of C-C and C=C modes are identified at low fluences. The IR active modes with increased intensity indicates the increased conjugation length, while the XRD analysis revels the improved crystallinity with enhanced molecular ordering. The XPS analysis shows that chemical bonding nature near the film surface is not affected by irradiation. The room temperature electrical conductivity is found to be increased from 2.48 × 10−6 to 1.35 × 10−5 Ω−1cm−1 at the fluence of 1 × 1010 ions/cm2. The temperature dependence of dc conductivity has been explained using Mott's variable range hopping model. SAXS detector images confirm the presence of ion tracks and density variation between the track core and halo regions. It is found that less intense heating effect in the halo region of ion path could induce the molecular ordering of P3HT. © 2016 Elsevier Ltd