Conductive poly(3,4-ethylenedioxythiophene)/TiO2 nanocomposites were synthesized via a facile oxidative polymerization approach using dodecylbenzene sulfonic acid as a dopant and ammonium peroxydisulfate as an oxidant and irradiated with 90 MeV O7+ ions at the fluences of 5 × 1010, 1 × 1011, 5 × 1011, and 1 × 1012 ions cm−2 using 15UD Pelletron accelerator under high vacuum. X-ray diffraction studies show that microstrain and domain crystallite size of the nanocomposites increases with the increase of ion fluence resulting in highly ordered PEDOT-TiO2 nanocomposites. Thermogravimmetric analysis shows that the thermal stability of the nanocomposites increases with the increase of irradiation fluences which can be attributed to the crosslinking of polymer chains due to high electronic energy deposition. Scanning electron micrographs show that there is grain growth after swift heavy ion (SHI) irradiation resulting highly dense and less porous microstructure of nanocomposite films. DC conductivity of unirradiated nanocomposites exhibits Mott's 1D variable range hopping (VRH) mechanism. However, there is cross over to 3D VRH mechanism at higher irradiation fluence of 5 × 1011 and 1 × 1012 ions cm−2. There is an enhancement in the electrical conductivity of the nanocomposites upon SHI irradiation correlating crosslinking with DC conductivity of the nanocomposites.