Two-photon absorption (TPA) of Au-ion irradiated glasses in the femtosecond regime has been analyzed by an open-aperture Z scan technique. Three types of glasses, namely GIL49, BK7, and Glass B were irradiated by using 1700 keV Au+ ion beams. Samples were post-annealed at 600°C for 5 h. Penetration depth and distribution of Au+ ions having 1700 keV energy within glass substrates were estimated by transport of ions in matter (TRIM) simulations. Detailed calculations with full-damage cascades were performed for each sample, taking into account the chemical composition of glass substrates. TRIM results reveal that there is no significant change in ion range, straggling, and ion distribution with the change in the substrate composition. However, Z scan results showed a difference in TPA coefficients for all three glasses. Extent of crosslinking within each of irradiated sample, owing to its chemical composition, may have affected their TPA coefficients.