The invention discloses a method for preparing fullerene oxide modified silica gel. The method comprises the following steps: (1) adding silica gel, of which the surface contains silicon hydroxyl, into a solvent, i.e., toluene, carrying out uniform mixing, then, adding aminopropyl triethoxysilane into the mixture, carrying out heating reflux, and carrying out amination on the surface of the silica gel, so as to obtain aminopropyl silica gel; (2) adding fullerene into an acid mixture consisting of concentrated nitric acid and concentrated sulfuric acid, and carrying out standing oxidation treatment, so as to obtain fullerene oxide; and (3) dispersing the fullerene oxide into water, carrying out uniform mixing, then, adding the aminopropyl silica gel into the mixture, and carrying out surface covalent bonding, thereby obtaining the fullerene oxide modified silica gel. The fullerene oxide modified silica gel prepared by the method can be applied to the separation analysis of substances as chromatographic packing; and the chromatographic packing has the excellent physical structure of a silica-gel substrate, has the special chromatographic performance of the fullerene oxide and has very high polarity and hydrophilicity.