We report here experimental results investigating the influence of the initial swift heavy ion charge on the structure of polyethylene terephthalate (PET) film after irradiation, using a structurally sensitive X-ray diffraction method. Kr ions with an energy of 100 MeV and charges of 13+, 14+, and 15+ were each used at irradiation fluences of 5 × 1010, 7.5 × 1010, 1 × 1011, 2.5 × 1011 and 5 × 1011 ions/cm2. At constant energy and irradiation fluence, the post-irradiation structural changes in PET film show a clear dependence on the initial ion charge. As either the fluence or ion charge increase, the latent tracks begin to overlap, leading to cross-linking of PET chain molecules to form rotational isomers (rotamers). We use the fluence corresponding to the onset of overlapping to estimate the size of latent tracks for different ion charges. At the highest fluences, the latent tracks become entirely overlapped, and the interchain cross-linking extends throughout the whole film. Since this cross-linking is due to the dipole–dipole interaction of subunits of repeat units of PET chain molecules, it is reversible, in contrast to the well-known chemical cross-linking of polymer chain molecules under irradiation.