Considering the future perspectives of room temperature ionic liquids (RTILs) in areas involving high radiation fields (such as the nuclear fuel cycle and space applications), it is essential to probe and have a microscopic understanding of the radiation induced perturbations in the molecular structures and the intrinsic bonding interactions existing in the ILs. Herein, a focused investigation concerning the photophysical behavior of post-irradiated FAP (fluoroalkyl phosphate) imidazolium ILs revealed considerable rearrangements and bonding realignments of the ionic moieties in the ILs on irradiation, however, their physicochemical properties do not change significantly even at high absorbed doses. Most interestingly, the well-established excitation wavelength dependent fluorescence (FL) behavior of the ILs was considerably perturbed on irradiation and this is attributed to the radiation induced decoupling of pre-existing different associated structures of ions, and the subsequent formation of oligomers and other species containing multiple bond order groups. This was further substantiated by vibrational studies, where peaks appearing in the range 1600-1800 cm(-1) indicated the formation of double bonded products. Furthermore, for the hydroxyl functionalized (in the alkyl side chain of the imidazolium cation) IL, a blue shift in the O-H stretching frequency was observed for the -OH group H-bonded to the FAP anion (νOH···[FAP](-)), while a red shift was observed for the H-bonded -OH groups in the cationic clusters. The FL lifetime values were found to increase with irradiation, which clearly indicates the enhancement in the rigidity level in the vicinity of the ions, thereby hindering the non-radiative decay processes. Such studies could contribute to the fundamental understanding of the radiation driven perturbations in the structure-property relationships, which eventually affect the radiolytic degradation pathways and the product distribution in RTILs.