X-ray photoelectron and near-edge X-ray absorption fine structure (NEXAFS) spectra, as well as the ground-state electronic/geometrical structures of a newly discovered nonclassical isomer C 2 v -C 66(NC), and two classical fullerene isomers C 2- #4466C 66 and C s - #4169C 66 with their hydrogenated derivatives [ C 2 v -C 66H 4(NC), C 2- #4466C 66H 4, and C s - #4169C 66H 4] have been calculated at the density functional theory (DFT) level. Significant differences were observed in the electronic structures and simulated X-ray spectra after hydrogenation. Simultaneously, both X-ray photoelectron and NEXAFS spectra reflected conspicuous isomer dependence, indicating that the “fingerprints” in the X-ray spectra can offer an effective method for identifying the above-mentioned fullerene isomers. The simulated ultraviolet–visible (UV–vis) absorption spectroscopy of C 2 v -C 66H 4(NC) has also been generated by means of the time-dependent DFT method, and the calculations are well consistent with the experimental results. Consequently, this work reveals that X-ray and UV–vis spectroscopy techniques can provide valuable information to help researchers explore the fullerene electronic structure and isomer identification on the future experimental and theoretical fullerene domains.