The effect of crystal structural inhomogeneities in the form of β-phases, metamict phases, as well as point defects and impurities on the kinetics of phase transformations and amorphization occurring in quartz crystals under neutron irradiation has not been sufficiently investigated.For this reason, the kinetics of gamma-luminescence (GL) and photoluminescence (FL) bands in quartz crystals grown on seeds irradiated with neutrons at a dose of 5*1018, 1019 and 5*1019 n/cm2 after additional neutron irradiation of 1016-8*1020n/cm2 in the temperature range of 77-300 K. Based on the analysis of luminescent properties, the nature of intrinsic defects in the structure of quartz crystals, their role in the formation of color and glow centers, has been studied. Based on the analysis of experimental data, the study of the luminescent properties of quartz crystals determined the properties of various centers of luminescence and the formation of color centers of crystalline quartz.