Preparation of amorphous silica doped with organic dye molecules, 1,4‐dihydroxyanthraquinone, and the observation of the amorphous structure of this system by photochemical hole burning using the dye molecules as a spectral probe are reported. The various kinds of organic molecule‐doped inorganic glassy materials are obtained with the alcoholate method. The appearance of the photochemical hole in this system shows the molecular dispersion of the dye molecules in the matrix without cracking or decomposition. The burning yield, 1.2×10−4, is the same as that observed in organic glasses. The intrinsic holewidth, 0.9 cm−1at zero burning time limit, the burning‐time dependence and the annealing effects on the hole profile were observed and compared with those in the alcoholic organic glass. It is suggested that the nearest‐neighbor structures around quinizarin molecules consist of some hydroxyl groups. The matrix cages seem to be fairly tight and rigid in comparison with those of the alcoholic glass. The possibility that the quinizarin molecule or molecules are embedded within the pore of amorphous SiO2with some amount of solvent molecules, mainly ethanol or water, seems to be excluded. The annealing effects of the burned hole indicate that there exist two kinds of mechanisms which dominate the temperature dependence of the holewidth in the present system. One is already dominant below about 27 K which gives rise to the reversible behavior in the holewidth with temperature, and the other becomes effective above 27 K and is irreversible with temperature cycling. Some discussions are given on the origin of these relaxation mechanisms in this system which are inherent in the structure of amorphous materials.