Core-level and valence-band X-ray photoelectron spectroscopy was employed to study the dose-dependent radiation effects in the short-range order and the electronic structure of natural U, Th-bearing zircon near-surface layers. Single crystals from different localities (Ratanakiri, Cambodia; Mud Tank, Australia; Highlands, Sri Lanka) exhibiting wide variations in the accumulated radiation dose D≈(0 ÷ 9.2)·1018 α-decays/g was investigated. The dose values obtained by electron probe microanalysis and Raman micro-spectroscopy were used to correlate the samples with the two percolation transitions (p1, p2) in the amorphous-crystalline structure of damaged zircon. The dose-dependent variations in Eb (530.9–531.3, 101.7–102.4, 182.8- 183.3 eV) and FWHM (1.32–2.57, 1.47–1.77, 1.16 -1.55 eV) of the O1s, Si2p, and Zr3d5/2 core levels, respectively, were attributed to changes in the ensemble of non-equivalent short-range order structures. An increase in the dose resulted in the complication of the oxygen sublattice, with the following nearest environments of O atoms: (1) O (Si, [8]Zr, [8]Zr), Eb = 530.8–531.2 eV, the amount of > ~3.5 apfu (at D p2). For the first time, under an increase in the radiation dose, the oppositely directed changes in the effective charges of Si and Zr cations were detected in damaged zircon. This phenomenon was assigned to an increase in the content of the short-range order fragments characteristic of pure oxides SiO2 (namely, Si-O-Si) and ZrO2 (namely, [7]Zr) as well as to the influence of the anions O (Si, Si, [8]Zr), and the assignment was independently confirmed by the valence band analysis. The sequence of transformations in the Si-O and Zr-O sublattices was shown to be not concurrent: a partial polymerization of SiO4 tetrahedra occurs mainly at low and medium doses (D p2) in the amorphous fraction.