We study the room-temperature (RT) pulsed cathodoluminescence (PCL) spectrum of a high-purity synthetic α-quartz single crystal. The spectrum consists of two wide bands with intensity maxima at 415 and 490 nm (2.99 and 2.53 eV). The band at 490 nm (2.5 eV) is polarized in the XY crystal plane (perpendicular to the third-order symmetry axis) and possesses a structure with three peaks at 480±2, 487±2, and 493±2 nm (2.58±0.01, 2.55±0.01, and 2.52±0.01 eV). The intensities of the peaks at 480±2 and 493±2 nm increased with increase in the irradiation dose up to 45 kGy. Peaks are equidistant at the energetic scale. The energy separation between the peaks Δ = 0.03 ± 0.01 eV is equal in order of magnitude to energies of Li x O y molecular vibrations and to the energy of the optical phonon in α-quartz. We propose an explanation of the experimental data obtained. According to this explanation, the structure observed may be attributed to the amplitude modulation of the quartz 2.5 eV emission band by the crystalline electric fields on frequencies of optical phonons. The nonequilibrium phonons may arise during the electron-beam irradiation.