Influence of Oxygen ions (100MeV) irradiation on Polyaniline (PANI)/Single Walled Carbon Nanotubes (SWNTs) nanocomposite was studied in the present investigation. PANI/SWNTs nanocomposite was synthesized by electrochemical Cyclic Voltammetry technique. Nanocomposite was exposed under SHI irradiation of Oxygen (100MeV) ions for three different fluences such as 1×1010ions/cm2, 5×1010ions/cm2 and 1×1011ions/cm2. The SHI irradiated PANI/SWNTs nanocomposite was investigated by using morphological (AFM), structural (XRD) and spectroscopy (FTIR) characterization. AFM study exhibits effects of SHI irradiation on morphology of the nanocomposite and root mean square roughness of the nanocomposite is observed to be decreased as fluence was increased. The FTIR absorption spectrum exhibits formation of new functional sites with the increase in intensity of absorption peaks, due to SHI irradiation. X-Ray Diffraction studies show a gradual decrease in the crystalline nature of the nanocomposite upon irradiation.