The invention relates to a method for preparing a substrate material with a multilayer composite protective film, which comprises the following steps: putting the substrate material into a reaction chamber, and heating the substrate material until the temperature thereof is 100 to 500 DEG C; introducing trimethyl aluminum or Al (CH3) N (CH2) 5CH3 precursor into the reaction chamber within 0.2 to 0.5 seconds under the pressure of 0.1 to 10 Torr; introducing nitrogen or inert gas into the reaction chamber so as to remove the trimethyl aluminum or Al (CH3) N (CH2) 5CH3 residual gas which is not subjected to chemisorption by a substrate; under the pressure of 0.1 to 10 Torr, introducing ozone or vapor reactive gas into the reaction chamber within 0.2 to 0.5 seconds so as to deposit an alumina atom layer on the substrate, wherein the thickness of the alumina atom layer on the substrate is 2 to 100nm; and replacing the trimethyl aluminum or Al (CH3) N (CH2) 5CH3 precursor by using chlorosilane, hexachlorodisilane or tetraethyl orthosilicate as silicon source, then repeating the steps above, and covering a silicon dioxide layer on an alumina layer, wherein the thickness of the alumina layer is 2 to 100nm; and finally, obtaining the substrate material with a composite inorganic protective film in a Al2O3/SiO2 double-layer structure, wherein the thickness of the substrate material is 5 to 120nm. The method can precisely control the thickness of the film, wherein the thickness of the film can directly and precisely be controlled within a range of 1 to 100nm, and the film has excellent oxidation resistance and gas permeation resistance, and can control the ratio of Al2O3 to SiO2.